R Bootcamp Einstein 2017
Michoel Snow
August 8 & 10, 2017
SECTION 1 - The Basics
Installing R
If you don’t have them already installed you need to download and install R and R studio
- Download R
- R Studio
Introduction to R
- R is an open source programming environment
- It is most commonly used for statistical computing and graphics
- The basic functionality of R can be extended with ‘packages’
- Reusable R functions and their documentation
- Often times will include sample data.
Resources for R
- R for data science http://r4ds.had.co.nz
- Served as inspiration for a lot of this bootcamp
- Written by programmers at R Studio
- R Programming for Data Science https://bookdown.org/rdpeng/rprogdatascience/
- R Bootcamp https://www.jaredknowles.com/r-bootcamp/
Introduction to R studio
- R studio is an IDE within which you can write/edit code, run code, display plots/graphics and a whole host of other functions
Getting Started
- Go to https://github.com/mseinstein/ to download the Presentions > RBootCamp > r_bootcamp_einstein_2017.R file
- All the code presented here is within that R file
What can you do with R
- Analytics
- Mathematics, Probability and Statistics
- Big Data Analytics
- Statistical Modeling
- Machine Learning
- Visualizations
- Simple but powerful graphics packages
- Applications and Extensions
- Web applications (Shiny)
- Bioinformatics/Genomics (Bioconductor)
- Research Friendly
- Reproducible Results
- Strong Link to Academia
Objectives of this Bootcamp
By the end of this bootcamp, students should be able to
- Identify projects and tasks suitable to R
- Use Rstudio as a frontend for R programming
- Import data from outside sources into R
- Manipulate data and perform basic analysis
- Create and export visualizations of data
- Modify pre-written R code for their own applications
Structure of This Bootcamp
- Visualization of Data
- Manipulation of Data
- Importing/cleaning of Data
Running code in R
- To run any line of code use CTRL+Enter or Cmd+Enter
- R will run the highlighted code OR
- R will run the line of code which the cursor is on
Installing and Loading packages
- The power of R can be extended with packages
- You install a package with the
install.packages("Pkg Name"), e.g.,install.packages("tidyverse")- Only needs to be done once per machine
- Tidyverse is a collection of R packages for data manipulation and visualization that are designed to work together
- This is the main package we will be using
- To load a package call the
libraryfunction, e.g.,library(tidyverse)- Needs to be loaded every session you want to use it (usually everytime you open R studio)
Key Symbols
- < -
- Assignment operator, e.g. x <- 5
- The equals sign, =, will work as a substitution in most but not all cases
#- Denotes a comment
- All text following the
#will be ignored
?function_name- Opens the Documentation for the function
??term- Searches the help documentation for the queried string
Brief Aside 1
RXKCD
SECTION 2 - Data Visualisations
ggplot2
- ggplot2 is a plotting system for R, based on the grammar of graphics
- See http://vita.had.co.nz/papers/layered-grammar.pdf for an in-depth discussion
library(tidyverse)
Data visualization Cheat Sheet
- R studio provides helpful cheat sheets which you can bring up from the Help toolbar
- Open the Data visualization for ggplot2 cheat sheet
Graphics in ggplot are built in layers
Use the data visualization cheatsheet in the RStudio Help menu as a reference
ggplot(mpg,aes(x=hwy,y=cty)) +
geom_blank()
ggplot(mpg,aes(x=hwy,y=cty)) +
geom_blank() +
geom_abline()
ggplot(mpg,aes(x=hwy,y=cty)) +
geom_blank() +
geom_abline() +
geom_jitter(aes(color=class))
ggplot(mpg,aes(x=hwy,y=cty)) +
geom_blank() +
geom_abline() +
geom_jitter(aes(color=class)) +
geom_point(data=mpg_class,aes(x=hwy_mean,y=cty_mean,fill=class),color="black",size=5,shape=22,show.legend = FALSE) 
mpg dataset
# mpg is a ggplot dataset of fuel economy data from 1999 and 2008 for 38 popular models of car
mpg## # A tibble: 234 × 11
## manufacturer model displ year cyl trans drv cty hwy fl class
## <chr> <chr> <dbl> <int> <int> <chr> <chr> <int> <int> <chr> <chr>
## 1 audi a4 1.8 1999 4 auto(l5) f 18 29 p compact
## 2 audi a4 1.8 1999 4 manual(m5) f 21 29 p compact
## 3 audi a4 2.0 2008 4 manual(m6) f 20 31 p compact
## 4 audi a4 2.0 2008 4 auto(av) f 21 30 p compact
## 5 audi a4 2.8 1999 6 auto(l5) f 16 26 p compact
## 6 audi a4 2.8 1999 6 manual(m5) f 18 26 p compact
## 7 audi a4 3.1 2008 6 auto(av) f 18 27 p compact
## 8 audi a4 quattro 1.8 1999 4 manual(m5) 4 18 26 p compact
## 9 audi a4 quattro 1.8 1999 4 auto(l5) 4 16 25 p compact
## 10 audi a4 quattro 2.0 2008 4 manual(m6) 4 20 28 p compact
## # ... with 224 more rowssummary(mpg)## manufacturer model displ year cyl trans
## Length:234 Length:234 Min. :1.600 Min. :1999 Min. :4.000 Length:234
## Class :character Class :character 1st Qu.:2.400 1st Qu.:1999 1st Qu.:4.000 Class :character
## Mode :character Mode :character Median :3.300 Median :2004 Median :6.000 Mode :character
## Mean :3.472 Mean :2004 Mean :5.889
## 3rd Qu.:4.600 3rd Qu.:2008 3rd Qu.:8.000
## Max. :7.000 Max. :2008 Max. :8.000
## drv cty hwy fl class
## Length:234 Min. : 9.00 Min. :12.00 Length:234 Length:234
## Class :character 1st Qu.:14.00 1st Qu.:18.00 Class :character Class :character
## Mode :character Median :17.00 Median :24.00 Mode :character Mode :character
## Mean :16.86 Mean :23.44
## 3rd Qu.:19.00 3rd Qu.:27.00
## Max. :35.00 Max. :44.00mpg$drv## [1] "f" "f" "f" "f" "f" "f" "f" "4" "4" "4" "4" "4" "4" "4" "4" "4" "4" "4" "r" "r" "r" "r" "r" "r" "r" "r" "r" "r"
## [29] "4" "4" "4" "4" "f" "f" "f" "f" "f" "f" "f" "f" "f" "f" "f" "f" "f" "f" "f" "f" "4" "4" "4" "4" "4" "4" "4" "4"
## [57] "4" "4" "4" "4" "4" "4" "4" "4" "4" "4" "4" "4" "4" "4" "4" "4" "4" "4" "r" "r" "r" "4" "4" "4" "4" "4" "4" "4"
## [85] "4" "4" "4" "4" "4" "4" "r" "r" "r" "r" "r" "r" "r" "r" "r" "f" "f" "f" "f" "f" "f" "f" "f" "f" "f" "f" "f" "f"
## [113] "f" "f" "f" "f" "f" "f" "f" "f" "f" "f" "4" "4" "4" "4" "4" "4" "4" "4" "4" "4" "4" "4" "r" "r" "r" "4" "4" "4"
## [141] "4" "f" "f" "f" "f" "f" "f" "f" "f" "f" "4" "4" "4" "4" "f" "f" "f" "f" "f" "4" "4" "4" "4" "4" "4" "4" "4" "4"
## [169] "4" "4" "4" "4" "4" "4" "4" "4" "4" "4" "4" "f" "f" "f" "f" "f" "f" "f" "f" "f" "f" "f" "f" "f" "f" "f" "f" "f"
## [197] "f" "f" "4" "4" "4" "4" "4" "4" "4" "4" "4" "f" "f" "f" "f" "f" "f" "f" "f" "f" "f" "f" "f" "f" "f" "f" "f" "f"
## [225] "f" "f" "f" "f" "f" "f" "f" "f" "f" "f"ggplot command
The ggplot command begins a plot to which you can add layers
ggplot(data = mpg)
ggplot(data = mpg) +
geom_point(mapping = aes(x = displ, y = hwy))
ggplot(data = mpg) +
geom_smooth(mapping = aes(x = displ, y = hwy)) +
geom_point(mapping = aes(x = displ, y = hwy))
Variable propagation
By inserting x and y into ggplot, all layers will use those parameters unless otherwise specified
ggplot(data = mpg, mapping = aes(x = displ, y = hwy)) +
geom_smooth() +
geom_point()
ggplot(data = mpg, mapping = aes(x = displ, y = hwy)) +
geom_smooth() +
geom_point() +
geom_smooth(mapping = aes(x = displ,y = cty),color = "red")
Features vs Variables
Note: if you want to plot a variable to a feature like color or size, it must go in the aes() term, if you just want to set them at a certain value they go outside the aes
ggplot(mpg, aes(displ,hwy)) +
geom_smooth(color = "green") +
geom_point(aes(color=class),size=2)
Facets
You can also split the plot into subplots based on a varible using facet
ggplot(mpg, aes(displ,hwy)) +
geom_point() +
facet_grid(.~cyl)
ggplot(mpg, aes(displ,hwy)) +
geom_point() +
facet_grid(cyl~.)
ggplot(mpg, aes(displ,hwy)) +
geom_point() +
facet_wrap(~cyl)
ggplot(mpg, aes(displ,hwy)) +
geom_point() +
facet_grid(cyl~class)
Exercises
Try to make some of the following plots:
Graphics and Statistical Transformations
This time we will be using the diamonds dataset
diamonds## # A tibble: 53,940 × 10
## carat cut color clarity depth table price x y z
## <dbl> <ord> <ord> <ord> <dbl> <dbl> <int> <dbl> <dbl> <dbl>
## 1 0.23 Ideal E SI2 61.5 55 326 3.95 3.98 2.43
## 2 0.21 Premium E SI1 59.8 61 326 3.89 3.84 2.31
## 3 0.23 Good E VS1 56.9 65 327 4.05 4.07 2.31
## 4 0.29 Premium I VS2 62.4 58 334 4.20 4.23 2.63
## 5 0.31 Good J SI2 63.3 58 335 4.34 4.35 2.75
## 6 0.24 Very Good J VVS2 62.8 57 336 3.94 3.96 2.48
## 7 0.24 Very Good I VVS1 62.3 57 336 3.95 3.98 2.47
## 8 0.26 Very Good H SI1 61.9 55 337 4.07 4.11 2.53
## 9 0.22 Fair E VS2 65.1 61 337 3.87 3.78 2.49
## 10 0.23 Very Good H VS1 59.4 61 338 4.00 4.05 2.39
## # ... with 53,930 more rowssummary(diamonds)## carat cut color clarity depth table price
## Min. :0.2000 Fair : 1610 D: 6775 SI1 :13065 Min. :43.00 Min. :43.00 Min. : 326
## 1st Qu.:0.4000 Good : 4906 E: 9797 VS2 :12258 1st Qu.:61.00 1st Qu.:56.00 1st Qu.: 950
## Median :0.7000 Very Good:12082 F: 9542 SI2 : 9194 Median :61.80 Median :57.00 Median : 2401
## Mean :0.7979 Premium :13791 G:11292 VS1 : 8171 Mean :61.75 Mean :57.46 Mean : 3933
## 3rd Qu.:1.0400 Ideal :21551 H: 8304 VVS2 : 5066 3rd Qu.:62.50 3rd Qu.:59.00 3rd Qu.: 5324
## Max. :5.0100 I: 5422 VVS1 : 3655 Max. :79.00 Max. :95.00 Max. :18823
## J: 2808 (Other): 2531
## x y z
## Min. : 0.000 Min. : 0.000 Min. : 0.000
## 1st Qu.: 4.710 1st Qu.: 4.720 1st Qu.: 2.910
## Median : 5.700 Median : 5.710 Median : 3.530
## Mean : 5.731 Mean : 5.735 Mean : 3.539
## 3rd Qu.: 6.540 3rd Qu.: 6.540 3rd Qu.: 4.040
## Max. :10.740 Max. :58.900 Max. :31.800
## ggplot(diamonds, aes(cut)) + geom_bar()
ggplot(diamonds, aes(price)) + geom_histogram(bins = 100)
Computed Variables
- Bar charts, histograms and the other plots in the one variable section of the ggplot2 cheat sheet bin your data based on a single variable
- You can determine the computed variables of a graphic by using the help function:
- Computed variables
- count
- Number of points in bin
- prop
- Groupwise proportion
- count
- Computed variables
ggplot(diamonds) + geom_bar(aes(x = cut, y = ..count.., group = 1))
ggplot(diamonds) + geom_bar(aes(x = cut, y = ..prop.., group = 1))
Position adjustments
ggplot(diamonds) + geom_bar(aes(x = color, fill = cut), position = "dodge")
ggplot(diamonds) + geom_bar(aes(x = color, fill = cut), position = "fill")
ggplot(diamonds) + geom_bar(aes(x = color, color = cut), position = "stack", fill = NA)
Example Plots
plots from http://r-statistics.co/Top50-Ggplot2-Visualizations-MasterList-R-Code.html
ggplot(midwest, aes(x=area, y=poptotal)) +
geom_point(aes(col=state, size=popdensity)) +
geom_smooth(method="loess", se=F) + xlim(c(0, 0.1)) + ylim(c(0, 500000)) +
labs(subtitle="Area Vs Population", y="Population", x="Area", title="Scatterplot", caption = "Source: midwest")
mtcars$`car name` <- rownames(mtcars) # create new column for car names
mtcars$mpg_z <- round((mtcars$mpg - mean(mtcars$mpg))/sd(mtcars$mpg), 2) # compute normalized mpg
mtcars$mpg_type <- ifelse(mtcars$mpg_z < 0, "below", "above") # above / below avg flag
mtcars <- mtcars[order(mtcars$mpg_z), ] # sort
mtcars$`car name` <- factor(mtcars$`car name`, levels = mtcars$`car name`) # convert to factor to retain sorted order in plot.
ggplot(mtcars, aes(x=`car name`, y=mpg_z, label=mpg_z)) +
geom_bar(stat='identity', aes(fill=mpg_type), width=.5) +
scale_fill_manual(name="Mileage",
labels = c("Above Average", "Below Average"),
values = c("above"="#00ba38", "below"="#f8766d")) +
labs(subtitle="Normalised mileage from 'mtcars'", title= "Diverging Bars") +
coord_flip()
# prep data
df <- read.csv("https://raw.githubusercontent.com/selva86/datasets/master/gdppercap.csv")
colnames(df) <- c("continent", "1952", "1957")
left_label <- paste(df$continent, round(df$`1952`),sep=", ")
right_label <- paste(df$continent, round(df$`1957`),sep=", ")
df$class <- ifelse((df$`1957` - df$`1952`) < 0, "red", "green")
ggplot(df) + geom_segment(aes(x=1, xend=2, y=`1952`, yend=`1957`, col=class), size=.75, show.legend=F) +
geom_vline(xintercept=1, linetype="dashed", size=.1) +
geom_vline(xintercept=2, linetype="dashed", size=.1) +
scale_color_manual(labels = c("Up", "Down"),
values = c("green"="#00ba38", "red"="#f8766d")) + # color of lines
labs(x="", y="Mean GdpPerCap") + # Axis labels
xlim(.5, 2.5) + ylim(0,(1.1*(max(df$`1952`, df$`1957`)))) + # X and Y axis limits
geom_text(label=left_label, y=df$`1952`, x=rep(1, NROW(df)), hjust=1.1, size=3.5) +
geom_text(label=right_label, y=df$`1957`, x=rep(2, NROW(df)), hjust=-0.1, size=3.5) +
geom_text(label="Time 1", x=1, y=1.1*(max(df$`1952`, df$`1957`)), hjust=1.2, size=5) + # title
geom_text(label="Time 2", x=2, y=1.1*(max(df$`1952`, df$`1957`)), hjust=-0.1, size=5) + # title
theme(panel.background = element_blank(),panel.grid = element_blank(),axis.ticks = element_blank(),
axis.text.x = element_blank(),panel.border = element_blank(),plot.margin = unit(c(1,2,1,2), "cm"))
ggplot(mpg, aes(cty)) +
geom_density(aes(fill=factor(cyl)), alpha=0.8) +
labs(title="Density plot",
subtitle="City Mileage Grouped by Number of cylinders",
caption="Source: mpg",
x="City Mileage",
fill="# Cylinders")
ggplot(mpg, aes(class, cty)) +
geom_violin() +
labs(title="Violin plot",
subtitle="City Mileage vs Class of vehicle",
caption="Source: mpg",
x="Class of Vehicle",
y="City Mileage")
theme_set(theme_classic())
df <- as.data.frame(table(mpg$class))
colnames(df) <- c("class", "freq")
ggplot(df, aes(x = "", y=freq, fill = factor(class))) +
geom_bar(width = 1, stat = "identity") +
theme(axis.line = element_blank(),
plot.title = element_text(hjust=0.5)) +
labs(fill="class",
x=NULL,
y=NULL,
title="Pie Chart of class",
caption="Source: mpg") +
coord_polar(theta = "y", start=0)
EncSz <- 25
SynPermCon <- 0.5
PtPrcnt <- 0.75
SPSmpSz <- round(EncSz^2*PtPrcnt)
ENC <- rep(.3,EncSz^2)
ENC[c(19:83,200:250,353:420,497:585)] <- 1
SPEncBoxes <- tibble(x = rep(c(1:EncSz),EncSz), y = sort(rep(c(1:EncSz),EncSz)))
j <- rep(NA,EncSz^2)
j[sample(EncSz^2,SPSmpSz)] <- rnorm(SPSmpSz,mean=.9*SynPermCon,sd=SynPermCon/5)
j2 <- rep(NA,EncSz^2)
j2[j>0.5] <- 1
j2[j>0.5 & ENC ==1] <- 2
j2[is.na(j)] <- NA
EncAct <- rep(0.1,EncSz^2)
EncAct[j>SynPermCon] <- 1
j <- cut(j,breaks = c(-Inf,seq(0.4,0.6,0.025),Inf))
BlnkGrph = theme(axis.line=element_blank(), axis.text.x=element_blank(), axis.text.y=element_blank(), axis.ticks=element_blank(), axis.title.x=element_blank(),
axis.title.y=element_blank(), legend.position="none", panel.background=element_blank(), panel.border=element_blank(), panel.grid.major=element_blank(),
panel.grid.minor=element_blank(), plot.background=element_blank(),plot.margin=grid::unit(c(0,0,0,0), "mm"))
SPEncBoxes %>% ggplot(aes(x,y,fill = factor(round(ENC)))) +
geom_tile(color = "gray",show.legend=FALSE) + BlnkGrph + coord_fixed() +
geom_point(aes(x,y, color = factor(j2)),shape = 16,na.rm=TRUE, size = 3) +
scale_fill_manual(values = c("white","blue")) + scale_shape_identity() +
scale_color_manual(values = c("black","green"))
SPEncBoxes %>% ggplot(aes(x,y,fill = j, color = EncAct)) +
geom_tile(show.legend=FALSE, size = 0.2,alpha=EncAct) + BlnkGrph + coord_fixed() +
scale_color_gradient(low="gray",high ="black") +
scale_fill_manual(values = c("red","red","red","red","orangered", "orange","yellow","lightgreen","green1","green1"),na.value="white")
Saving plots
ggsave(filename)allows you to save plots- It guesses the filetype based on the extension used in the
filenameparameter- You can manually set the extension using the
deviceparameter - options are: ‘eps’, ‘ps’, ‘tex’, ‘pdf’, ‘jpeg/jpg’, ‘tiff’, ‘png’, ‘bmp’, ‘svg’, ‘wmf’ (windows only)
- You can manually set the extension using the
- By default it saves the last plot displayed unless you change the
plotparameter
ggplot(mpg,aes(x=hwy,y=cty)) +
geom_blank() +
geom_abline() +
geom_jitter(aes(color=class)) +
geom_point(data=mpg_class,aes(x=hwy_mean,y=cty_mean,fill=class),color="black",size=5,shape=22,show.legend = FALSE) 
ggsave("./images/cars.jpg")## Saving 8 x 5 in imageknitr::include_graphics("./images/cars.jpg")
ggsave("./images/cars_halfscale.jpg",scale=0.5)## Saving 4 x 2.5 in imageknitr::include_graphics("./images/cars_halfscale.jpg")
ggsave("./images/cars_w10h10.jpg",width=10,height=10)
knitr::include_graphics("./images/cars_w10h10.jpg")
ggsave("./images/cars_w10h10in.jpg",width=10,height=10,units="in")
knitr::include_graphics("./images/cars_w10h10in.jpg")
ggsave("./images/cars_w10h10cm.jpg",width=10,height=10,units="cm")
knitr::include_graphics("./images/cars_w10h10cm.jpg")
Spend some time playing with ggplot
- See http://ggplot2.tidyverse.org/reference/ for a full list of functions in ggplot
- Here are a list of the datasets built into ggplot (use ?“dataset name” to find out more about the individual datasets)
- diamonds
- Prices of 50,000 round cut diamonds
- economics
- US economic time series
- faithfuld
- 2d density estimate of Old Faithful data
- midwest
- Midwest demographics
- mpg
- Fuel economy data from 1999 and 2008 for 38 popular models of car
- msleep
- An updated and expanded version of the mammals sleep dataset
- presidential
- Terms of 11 presidents from Eisenhower to Obama
- seals
- Vector field of seal movements
- txhousing
- Housing sales in TX
- luv_colours
- colors() in Luv space
- diamonds
SECTION 3 - Data Manipulation
Mathematical and Boolean Operators
-sqrt(25) + (5 + 3)/4 * 7 - 2^2## [1] 55%/%3 # Integer Division## [1] 15%%3 # Modulo (remainder after division)## [1] 25 == 6## [1] FALSE5 != 6## [1] TRUE83 > (25 >= 23)## [1] TRUE5 > 3 & 3 < 2## [1] FALSE5 > 3 | 3 < 2## [1] TRUEVectors and Sequences
1:4## [1] 1 2 3 4c(5, 3, 2, 1) # Creates a vector via concatenation (hence the c)## [1] 5 3 2 1c(12, 1:4, 6)## [1] 12 1 2 3 4 6seq(from = 1, t = 10, by = 2) # Creates a vector with the given paramters## [1] 1 3 5 7 9seq(1, 10, 2) # creates the same vector without naming the paramters## [1] 1 3 5 7 9seq(1, 10) # R uses the default values for any empty parameters## [1] 1 2 3 4 5 6 7 8 9 10seq(to = 10, by = 2)## [1] 1 3 5 7 9seq(by = 2, to = 10)## [1] 1 3 5 7 9c(seq(1, 10, 2), 25, 10)## [1] 1 3 5 7 9 25 10c(seq(1, 10, 2), 25, 10) > 12## [1] FALSE FALSE FALSE FALSE FALSE TRUE FALSEc(seq(1, 10, 2), 25, 10) * 2## [1] 2 6 10 14 18 50 20Variables and Assignment
x = 5 + 3
(x = 5 + 3)## [1] 8x <- 5 + 3
(x <- 5 + 3)## [1] 8- Terminology
- The term on the left hand side is referred to as an object
- The term on the right hand side is the object’s value
- The
<-is the assignment operator
y <- x
y## [1] 8x <- 5 + 3 > 2
x## [1] TRUEx <- seq(172, 23, -13)
x## [1] 172 159 146 133 120 107 94 81 68 55 42 29Indexing
- Indexing is locating values by their index/indices within an N dimensional object
- Unlike some other programming languages R starts at 1
- Note that indexing uses [], while functions, like
seq, use ()
x <- seq(172, 23, -13)
x[1]## [1] 172x[c(1, 3)]## [1] 172 146x[2:4]## [1] 159 146 133x[4:2]## [1] 133 146 159x[]## [1] 172 159 146 133 120 107 94 81 68 55 42 29x[-1]## [1] 159 146 133 120 107 94 81 68 55 42 29x[-c(1, 3)]## [1] 159 133 120 107 94 81 68 55 42 29x[x%%2 == 0]## [1] 172 146 120 94 68 42y <- x[x%%2 == 0]
y[9] <- 10
y## [1] 172 146 120 94 68 42 NA NA 10Built in Functions
x <- 1:20
mean(x)## [1] 10.5max(x)## [1] 20min(x)## [1] 1length(x)## [1] 20range(x)## [1] 1 20prod(x)## [1] 2.432902e+18var(x)## [1] 35log(x)## [1] 0.0000000 0.6931472 1.0986123 1.3862944 1.6094379 1.7917595 1.9459101 2.0794415 2.1972246 2.3025851 2.3978953
## [12] 2.4849066 2.5649494 2.6390573 2.7080502 2.7725887 2.8332133 2.8903718 2.9444390 2.9957323sqrt(x)## [1] 1.000000 1.414214 1.732051 2.000000 2.236068 2.449490 2.645751 2.828427 3.000000 3.162278 3.316625 3.464102
## [13] 3.605551 3.741657 3.872983 4.000000 4.123106 4.242641 4.358899 4.472136Note that many functions in R have default values for some of their parameters and you should always try to be aware of them even if you don’t want to change them
rnorm(10)## [1] -0.49675197 0.34628110 0.77819899 -1.05046800 0.39643036 0.08076821 0.66607645 -1.56674161 -0.55028104
## [10] -0.96602903rnorm randomly generates values from a normal distribution, but a normal distribution requires a mean and a standard deviation. If you type ?rnorm you will see the full documentation but for our purposes the important part is
rnorm(n, mean = 0, sd = 1)
By default, the rnorm function assumes a mean of 0 and a standard deviation of 1. You can change those values easily, but only if you are aware of them.
Exercises
- Create a vector of 2 through 8 squared:
- 4, 9, 16, 25, 36, 49, 64
- Create a vector of the square roots of the sum of sqaures of every pair of digits of 1 to 100:
- sqrt(1^2 + 2^2), sqrt(3^2 + 4^2), sqrt(5^2 + 6^2), … , sqrt(99^2 + 100^2)
- Create a vector of the numbers 1 to 100 not divisible by 3 or 5:
- 1, 2, 4, 7, 8, 11, 13, 14, 16, 17, … , 97, 98
Data frames
When you have data consisting of multiple observations of multiple variables, i.e., a data set, this is most conveniently stored as a dataframe
iris # Famous iris data set which gives the measurements for 50 flowers from each of 3 species of iris## Sepal.Length Sepal.Width Petal.Length Petal.Width Species
## 1 5.1 3.5 1.4 0.2 setosa
## 2 4.9 3.0 1.4 0.2 setosa
## 3 4.7 3.2 1.3 0.2 setosa
## 4 4.6 3.1 1.5 0.2 setosa
## 5 5.0 3.6 1.4 0.2 setosa
## 6 5.4 3.9 1.7 0.4 setosa
## 7 4.6 3.4 1.4 0.3 setosa
## 8 5.0 3.4 1.5 0.2 setosa
## 9 4.4 2.9 1.4 0.2 setosa
## 10 4.9 3.1 1.5 0.1 setosa
## 11 5.4 3.7 1.5 0.2 setosa
## 12 4.8 3.4 1.6 0.2 setosa
## 13 4.8 3.0 1.4 0.1 setosa
## 14 4.3 3.0 1.1 0.1 setosa
## 15 5.8 4.0 1.2 0.2 setosa
## 16 5.7 4.4 1.5 0.4 setosa
## 17 5.4 3.9 1.3 0.4 setosa
## 18 5.1 3.5 1.4 0.3 setosa
## 19 5.7 3.8 1.7 0.3 setosa
## 20 5.1 3.8 1.5 0.3 setosa
## 21 5.4 3.4 1.7 0.2 setosa
## 22 5.1 3.7 1.5 0.4 setosa
## 23 4.6 3.6 1.0 0.2 setosa
## 24 5.1 3.3 1.7 0.5 setosa
## 25 4.8 3.4 1.9 0.2 setosa
## 26 5.0 3.0 1.6 0.2 setosa
## 27 5.0 3.4 1.6 0.4 setosa
## 28 5.2 3.5 1.5 0.2 setosa
## 29 5.2 3.4 1.4 0.2 setosa
## 30 4.7 3.2 1.6 0.2 setosa
## 31 4.8 3.1 1.6 0.2 setosa
## 32 5.4 3.4 1.5 0.4 setosa
## 33 5.2 4.1 1.5 0.1 setosa
## 34 5.5 4.2 1.4 0.2 setosa
## 35 4.9 3.1 1.5 0.2 setosa
## 36 5.0 3.2 1.2 0.2 setosa
## 37 5.5 3.5 1.3 0.2 setosa
## 38 4.9 3.6 1.4 0.1 setosa
## 39 4.4 3.0 1.3 0.2 setosa
## 40 5.1 3.4 1.5 0.2 setosa
## 41 5.0 3.5 1.3 0.3 setosa
## 42 4.5 2.3 1.3 0.3 setosa
## 43 4.4 3.2 1.3 0.2 setosa
## 44 5.0 3.5 1.6 0.6 setosa
## 45 5.1 3.8 1.9 0.4 setosa
## 46 4.8 3.0 1.4 0.3 setosa
## 47 5.1 3.8 1.6 0.2 setosa
## 48 4.6 3.2 1.4 0.2 setosa
## 49 5.3 3.7 1.5 0.2 setosa
## 50 5.0 3.3 1.4 0.2 setosa
## 51 7.0 3.2 4.7 1.4 versicolor
## 52 6.4 3.2 4.5 1.5 versicolor
## 53 6.9 3.1 4.9 1.5 versicolor
## 54 5.5 2.3 4.0 1.3 versicolor
## 55 6.5 2.8 4.6 1.5 versicolor
## 56 5.7 2.8 4.5 1.3 versicolor
## 57 6.3 3.3 4.7 1.6 versicolor
## 58 4.9 2.4 3.3 1.0 versicolor
## 59 6.6 2.9 4.6 1.3 versicolor
## 60 5.2 2.7 3.9 1.4 versicolor
## 61 5.0 2.0 3.5 1.0 versicolor
## 62 5.9 3.0 4.2 1.5 versicolor
## 63 6.0 2.2 4.0 1.0 versicolor
## 64 6.1 2.9 4.7 1.4 versicolor
## 65 5.6 2.9 3.6 1.3 versicolor
## 66 6.7 3.1 4.4 1.4 versicolor
## 67 5.6 3.0 4.5 1.5 versicolor
## 68 5.8 2.7 4.1 1.0 versicolor
## 69 6.2 2.2 4.5 1.5 versicolor
## 70 5.6 2.5 3.9 1.1 versicolor
## 71 5.9 3.2 4.8 1.8 versicolor
## 72 6.1 2.8 4.0 1.3 versicolor
## 73 6.3 2.5 4.9 1.5 versicolor
## 74 6.1 2.8 4.7 1.2 versicolor
## 75 6.4 2.9 4.3 1.3 versicolor
## 76 6.6 3.0 4.4 1.4 versicolor
## 77 6.8 2.8 4.8 1.4 versicolor
## 78 6.7 3.0 5.0 1.7 versicolor
## 79 6.0 2.9 4.5 1.5 versicolor
## 80 5.7 2.6 3.5 1.0 versicolor
## 81 5.5 2.4 3.8 1.1 versicolor
## 82 5.5 2.4 3.7 1.0 versicolor
## 83 5.8 2.7 3.9 1.2 versicolor
## 84 6.0 2.7 5.1 1.6 versicolor
## 85 5.4 3.0 4.5 1.5 versicolor
## 86 6.0 3.4 4.5 1.6 versicolor
## 87 6.7 3.1 4.7 1.5 versicolor
## 88 6.3 2.3 4.4 1.3 versicolor
## 89 5.6 3.0 4.1 1.3 versicolor
## 90 5.5 2.5 4.0 1.3 versicolor
## 91 5.5 2.6 4.4 1.2 versicolor
## 92 6.1 3.0 4.6 1.4 versicolor
## 93 5.8 2.6 4.0 1.2 versicolor
## 94 5.0 2.3 3.3 1.0 versicolor
## 95 5.6 2.7 4.2 1.3 versicolor
## 96 5.7 3.0 4.2 1.2 versicolor
## 97 5.7 2.9 4.2 1.3 versicolor
## 98 6.2 2.9 4.3 1.3 versicolor
## 99 5.1 2.5 3.0 1.1 versicolor
## 100 5.7 2.8 4.1 1.3 versicolor
## 101 6.3 3.3 6.0 2.5 virginica
## 102 5.8 2.7 5.1 1.9 virginica
## 103 7.1 3.0 5.9 2.1 virginica
## 104 6.3 2.9 5.6 1.8 virginica
## 105 6.5 3.0 5.8 2.2 virginica
## 106 7.6 3.0 6.6 2.1 virginica
## 107 4.9 2.5 4.5 1.7 virginica
## 108 7.3 2.9 6.3 1.8 virginica
## 109 6.7 2.5 5.8 1.8 virginica
## 110 7.2 3.6 6.1 2.5 virginica
## 111 6.5 3.2 5.1 2.0 virginica
## 112 6.4 2.7 5.3 1.9 virginica
## 113 6.8 3.0 5.5 2.1 virginica
## 114 5.7 2.5 5.0 2.0 virginica
## 115 5.8 2.8 5.1 2.4 virginica
## 116 6.4 3.2 5.3 2.3 virginica
## 117 6.5 3.0 5.5 1.8 virginica
## 118 7.7 3.8 6.7 2.2 virginica
## 119 7.7 2.6 6.9 2.3 virginica
## 120 6.0 2.2 5.0 1.5 virginica
## 121 6.9 3.2 5.7 2.3 virginica
## 122 5.6 2.8 4.9 2.0 virginica
## 123 7.7 2.8 6.7 2.0 virginica
## 124 6.3 2.7 4.9 1.8 virginica
## 125 6.7 3.3 5.7 2.1 virginica
## 126 7.2 3.2 6.0 1.8 virginica
## 127 6.2 2.8 4.8 1.8 virginica
## 128 6.1 3.0 4.9 1.8 virginica
## 129 6.4 2.8 5.6 2.1 virginica
## 130 7.2 3.0 5.8 1.6 virginica
## 131 7.4 2.8 6.1 1.9 virginica
## 132 7.9 3.8 6.4 2.0 virginica
## 133 6.4 2.8 5.6 2.2 virginica
## 134 6.3 2.8 5.1 1.5 virginica
## 135 6.1 2.6 5.6 1.4 virginica
## 136 7.7 3.0 6.1 2.3 virginica
## 137 6.3 3.4 5.6 2.4 virginica
## 138 6.4 3.1 5.5 1.8 virginica
## 139 6.0 3.0 4.8 1.8 virginica
## 140 6.9 3.1 5.4 2.1 virginica
## 141 6.7 3.1 5.6 2.4 virginica
## 142 6.9 3.1 5.1 2.3 virginica
## 143 5.8 2.7 5.1 1.9 virginica
## 144 6.8 3.2 5.9 2.3 virginica
## 145 6.7 3.3 5.7 2.5 virginica
## 146 6.7 3.0 5.2 2.3 virginica
## 147 6.3 2.5 5.0 1.9 virginica
## 148 6.5 3.0 5.2 2.0 virginica
## 149 6.2 3.4 5.4 2.3 virginica
## 150 5.9 3.0 5.1 1.8 virginicasummary(iris) # Very useful function, which gives summaries of each variable## Sepal.Length Sepal.Width Petal.Length Petal.Width Species
## Min. :4.300 Min. :2.000 Min. :1.000 Min. :0.100 setosa :50
## 1st Qu.:5.100 1st Qu.:2.800 1st Qu.:1.600 1st Qu.:0.300 versicolor:50
## Median :5.800 Median :3.000 Median :4.350 Median :1.300 virginica :50
## Mean :5.843 Mean :3.057 Mean :3.758 Mean :1.199
## 3rd Qu.:6.400 3rd Qu.:3.300 3rd Qu.:5.100 3rd Qu.:1.800
## Max. :7.900 Max. :4.400 Max. :6.900 Max. :2.500Matching
- You can call a single variable fo a dataframe using any of the following formats
dataset$variablenamedataset['variablename']dataset[variable column position]
names(iris)## [1] "Sepal.Length" "Sepal.Width" "Petal.Length" "Petal.Width" "Species"iris$Sepal.Length## [1] 5.1 4.9 4.7 4.6 5.0 5.4 4.6 5.0 4.4 4.9 5.4 4.8 4.8 4.3 5.8 5.7 5.4 5.1 5.7 5.1 5.4 5.1 4.6 5.1 4.8 5.0 5.0 5.2
## [29] 5.2 4.7 4.8 5.4 5.2 5.5 4.9 5.0 5.5 4.9 4.4 5.1 5.0 4.5 4.4 5.0 5.1 4.8 5.1 4.6 5.3 5.0 7.0 6.4 6.9 5.5 6.5 5.7
## [57] 6.3 4.9 6.6 5.2 5.0 5.9 6.0 6.1 5.6 6.7 5.6 5.8 6.2 5.6 5.9 6.1 6.3 6.1 6.4 6.6 6.8 6.7 6.0 5.7 5.5 5.5 5.8 6.0
## [85] 5.4 6.0 6.7 6.3 5.6 5.5 5.5 6.1 5.8 5.0 5.6 5.7 5.7 6.2 5.1 5.7 6.3 5.8 7.1 6.3 6.5 7.6 4.9 7.3 6.7 7.2 6.5 6.4
## [113] 6.8 5.7 5.8 6.4 6.5 7.7 7.7 6.0 6.9 5.6 7.7 6.3 6.7 7.2 6.2 6.1 6.4 7.2 7.4 7.9 6.4 6.3 6.1 7.7 6.3 6.4 6.0 6.9
## [141] 6.7 6.9 5.8 6.8 6.7 6.7 6.3 6.5 6.2 5.9iris["Sepal.Length"]## Sepal.Length
## 1 5.1
## 2 4.9
## 3 4.7
## 4 4.6
## 5 5.0
## 6 5.4
## 7 4.6
## 8 5.0
## 9 4.4
## 10 4.9
## 11 5.4
## 12 4.8
## 13 4.8
## 14 4.3
## 15 5.8
## 16 5.7
## 17 5.4
## 18 5.1
## 19 5.7
## 20 5.1
## 21 5.4
## 22 5.1
## 23 4.6
## 24 5.1
## 25 4.8
## 26 5.0
## 27 5.0
## 28 5.2
## 29 5.2
## 30 4.7
## 31 4.8
## 32 5.4
## 33 5.2
## 34 5.5
## 35 4.9
## 36 5.0
## 37 5.5
## 38 4.9
## 39 4.4
## 40 5.1
## 41 5.0
## 42 4.5
## 43 4.4
## 44 5.0
## 45 5.1
## 46 4.8
## 47 5.1
## 48 4.6
## 49 5.3
## 50 5.0
## 51 7.0
## 52 6.4
## 53 6.9
## 54 5.5
## 55 6.5
## 56 5.7
## 57 6.3
## 58 4.9
## 59 6.6
## 60 5.2
## 61 5.0
## 62 5.9
## 63 6.0
## 64 6.1
## 65 5.6
## 66 6.7
## 67 5.6
## 68 5.8
## 69 6.2
## 70 5.6
## 71 5.9
## 72 6.1
## 73 6.3
## 74 6.1
## 75 6.4
## 76 6.6
## 77 6.8
## 78 6.7
## 79 6.0
## 80 5.7
## 81 5.5
## 82 5.5
## 83 5.8
## 84 6.0
## 85 5.4
## 86 6.0
## 87 6.7
## 88 6.3
## 89 5.6
## 90 5.5
## 91 5.5
## 92 6.1
## 93 5.8
## 94 5.0
## 95 5.6
## 96 5.7
## 97 5.7
## 98 6.2
## 99 5.1
## 100 5.7
## 101 6.3
## 102 5.8
## 103 7.1
## 104 6.3
## 105 6.5
## 106 7.6
## 107 4.9
## 108 7.3
## 109 6.7
## 110 7.2
## 111 6.5
## 112 6.4
## 113 6.8
## 114 5.7
## 115 5.8
## 116 6.4
## 117 6.5
## 118 7.7
## 119 7.7
## 120 6.0
## 121 6.9
## 122 5.6
## 123 7.7
## 124 6.3
## 125 6.7
## 126 7.2
## 127 6.2
## 128 6.1
## 129 6.4
## 130 7.2
## 131 7.4
## 132 7.9
## 133 6.4
## 134 6.3
## 135 6.1
## 136 7.7
## 137 6.3
## 138 6.4
## 139 6.0
## 140 6.9
## 141 6.7
## 142 6.9
## 143 5.8
## 144 6.8
## 145 6.7
## 146 6.7
## 147 6.3
## 148 6.5
## 149 6.2
## 150 5.9iris[1]## Sepal.Length
## 1 5.1
## 2 4.9
## 3 4.7
## 4 4.6
## 5 5.0
## 6 5.4
## 7 4.6
## 8 5.0
## 9 4.4
## 10 4.9
## 11 5.4
## 12 4.8
## 13 4.8
## 14 4.3
## 15 5.8
## 16 5.7
## 17 5.4
## 18 5.1
## 19 5.7
## 20 5.1
## 21 5.4
## 22 5.1
## 23 4.6
## 24 5.1
## 25 4.8
## 26 5.0
## 27 5.0
## 28 5.2
## 29 5.2
## 30 4.7
## 31 4.8
## 32 5.4
## 33 5.2
## 34 5.5
## 35 4.9
## 36 5.0
## 37 5.5
## 38 4.9
## 39 4.4
## 40 5.1
## 41 5.0
## 42 4.5
## 43 4.4
## 44 5.0
## 45 5.1
## 46 4.8
## 47 5.1
## 48 4.6
## 49 5.3
## 50 5.0
## 51 7.0
## 52 6.4
## 53 6.9
## 54 5.5
## 55 6.5
## 56 5.7
## 57 6.3
## 58 4.9
## 59 6.6
## 60 5.2
## 61 5.0
## 62 5.9
## 63 6.0
## 64 6.1
## 65 5.6
## 66 6.7
## 67 5.6
## 68 5.8
## 69 6.2
## 70 5.6
## 71 5.9
## 72 6.1
## 73 6.3
## 74 6.1
## 75 6.4
## 76 6.6
## 77 6.8
## 78 6.7
## 79 6.0
## 80 5.7
## 81 5.5
## 82 5.5
## 83 5.8
## 84 6.0
## 85 5.4
## 86 6.0
## 87 6.7
## 88 6.3
## 89 5.6
## 90 5.5
## 91 5.5
## 92 6.1
## 93 5.8
## 94 5.0
## 95 5.6
## 96 5.7
## 97 5.7
## 98 6.2
## 99 5.1
## 100 5.7
## 101 6.3
## 102 5.8
## 103 7.1
## 104 6.3
## 105 6.5
## 106 7.6
## 107 4.9
## 108 7.3
## 109 6.7
## 110 7.2
## 111 6.5
## 112 6.4
## 113 6.8
## 114 5.7
## 115 5.8
## 116 6.4
## 117 6.5
## 118 7.7
## 119 7.7
## 120 6.0
## 121 6.9
## 122 5.6
## 123 7.7
## 124 6.3
## 125 6.7
## 126 7.2
## 127 6.2
## 128 6.1
## 129 6.4
## 130 7.2
## 131 7.4
## 132 7.9
## 133 6.4
## 134 6.3
## 135 6.1
## 136 7.7
## 137 6.3
## 138 6.4
## 139 6.0
## 140 6.9
## 141 6.7
## 142 6.9
## 143 5.8
## 144 6.8
## 145 6.7
## 146 6.7
## 147 6.3
## 148 6.5
## 149 6.2
## 150 5.9Indexing
- To call specific elements from the data set you can use either
- Variable indexing using the
$identifier, then using brackets after the variable name to indicate specific position(s)
- Two element indexing, where the first element is the row and the second element is the column (name or position)
- Variable indexing using the
iris$Sepal.Length[25:30]## [1] 4.8 5.0 5.0 5.2 5.2 4.7iris[25:30, "Sepal.Length"]## [1] 4.8 5.0 5.0 5.2 5.2 4.7iris[25:30, 1]## [1] 4.8 5.0 5.0 5.2 5.2 4.7iris[c(25:30, 17, 1), c(1, 4)]## Sepal.Length Petal.Width
## 25 4.8 0.2
## 26 5.0 0.2
## 27 5.0 0.4
## 28 5.2 0.2
## 29 5.2 0.2
## 30 4.7 0.2
## 17 5.4 0.4
## 1 5.1 0.2Trouble with Tibbles
Tibbles
- While the dataframes built into R are very useful, they are lacking in certain features
- Tibbles are a type of data frame that are lazy (they don’t change variable names or types) and surly (e.g., they complain when a variable does not exist)
- Tibbles differ from traditional data frames in two key ways, printing and subsetting
iris## Sepal.Length Sepal.Width Petal.Length Petal.Width Species
## 1 5.1 3.5 1.4 0.2 setosa
## 2 4.9 3.0 1.4 0.2 setosa
## 3 4.7 3.2 1.3 0.2 setosa
## 4 4.6 3.1 1.5 0.2 setosa
## 5 5.0 3.6 1.4 0.2 setosa
## 6 5.4 3.9 1.7 0.4 setosa
## 7 4.6 3.4 1.4 0.3 setosa
## 8 5.0 3.4 1.5 0.2 setosa
## 9 4.4 2.9 1.4 0.2 setosa
## 10 4.9 3.1 1.5 0.1 setosa
## 11 5.4 3.7 1.5 0.2 setosa
## 12 4.8 3.4 1.6 0.2 setosa
## 13 4.8 3.0 1.4 0.1 setosa
## 14 4.3 3.0 1.1 0.1 setosa
## 15 5.8 4.0 1.2 0.2 setosa
## 16 5.7 4.4 1.5 0.4 setosa
## 17 5.4 3.9 1.3 0.4 setosa
## 18 5.1 3.5 1.4 0.3 setosa
## 19 5.7 3.8 1.7 0.3 setosa
## 20 5.1 3.8 1.5 0.3 setosa
## 21 5.4 3.4 1.7 0.2 setosa
## 22 5.1 3.7 1.5 0.4 setosa
## 23 4.6 3.6 1.0 0.2 setosa
## 24 5.1 3.3 1.7 0.5 setosa
## 25 4.8 3.4 1.9 0.2 setosa
## 26 5.0 3.0 1.6 0.2 setosa
## 27 5.0 3.4 1.6 0.4 setosa
## 28 5.2 3.5 1.5 0.2 setosa
## 29 5.2 3.4 1.4 0.2 setosa
## 30 4.7 3.2 1.6 0.2 setosa
## 31 4.8 3.1 1.6 0.2 setosa
## 32 5.4 3.4 1.5 0.4 setosa
## 33 5.2 4.1 1.5 0.1 setosa
## 34 5.5 4.2 1.4 0.2 setosa
## 35 4.9 3.1 1.5 0.2 setosa
## 36 5.0 3.2 1.2 0.2 setosa
## 37 5.5 3.5 1.3 0.2 setosa
## 38 4.9 3.6 1.4 0.1 setosa
## 39 4.4 3.0 1.3 0.2 setosa
## 40 5.1 3.4 1.5 0.2 setosa
## 41 5.0 3.5 1.3 0.3 setosa
## 42 4.5 2.3 1.3 0.3 setosa
## 43 4.4 3.2 1.3 0.2 setosa
## 44 5.0 3.5 1.6 0.6 setosa
## 45 5.1 3.8 1.9 0.4 setosa
## 46 4.8 3.0 1.4 0.3 setosa
## 47 5.1 3.8 1.6 0.2 setosa
## 48 4.6 3.2 1.4 0.2 setosa
## 49 5.3 3.7 1.5 0.2 setosa
## 50 5.0 3.3 1.4 0.2 setosa
## 51 7.0 3.2 4.7 1.4 versicolor
## 52 6.4 3.2 4.5 1.5 versicolor
## 53 6.9 3.1 4.9 1.5 versicolor
## 54 5.5 2.3 4.0 1.3 versicolor
## 55 6.5 2.8 4.6 1.5 versicolor
## 56 5.7 2.8 4.5 1.3 versicolor
## 57 6.3 3.3 4.7 1.6 versicolor
## 58 4.9 2.4 3.3 1.0 versicolor
## 59 6.6 2.9 4.6 1.3 versicolor
## 60 5.2 2.7 3.9 1.4 versicolor
## 61 5.0 2.0 3.5 1.0 versicolor
## 62 5.9 3.0 4.2 1.5 versicolor
## 63 6.0 2.2 4.0 1.0 versicolor
## 64 6.1 2.9 4.7 1.4 versicolor
## 65 5.6 2.9 3.6 1.3 versicolor
## 66 6.7 3.1 4.4 1.4 versicolor
## 67 5.6 3.0 4.5 1.5 versicolor
## 68 5.8 2.7 4.1 1.0 versicolor
## 69 6.2 2.2 4.5 1.5 versicolor
## 70 5.6 2.5 3.9 1.1 versicolor
## 71 5.9 3.2 4.8 1.8 versicolor
## 72 6.1 2.8 4.0 1.3 versicolor
## 73 6.3 2.5 4.9 1.5 versicolor
## 74 6.1 2.8 4.7 1.2 versicolor
## 75 6.4 2.9 4.3 1.3 versicolor
## 76 6.6 3.0 4.4 1.4 versicolor
## 77 6.8 2.8 4.8 1.4 versicolor
## 78 6.7 3.0 5.0 1.7 versicolor
## 79 6.0 2.9 4.5 1.5 versicolor
## 80 5.7 2.6 3.5 1.0 versicolor
## 81 5.5 2.4 3.8 1.1 versicolor
## 82 5.5 2.4 3.7 1.0 versicolor
## 83 5.8 2.7 3.9 1.2 versicolor
## 84 6.0 2.7 5.1 1.6 versicolor
## 85 5.4 3.0 4.5 1.5 versicolor
## 86 6.0 3.4 4.5 1.6 versicolor
## 87 6.7 3.1 4.7 1.5 versicolor
## 88 6.3 2.3 4.4 1.3 versicolor
## 89 5.6 3.0 4.1 1.3 versicolor
## 90 5.5 2.5 4.0 1.3 versicolor
## 91 5.5 2.6 4.4 1.2 versicolor
## 92 6.1 3.0 4.6 1.4 versicolor
## 93 5.8 2.6 4.0 1.2 versicolor
## 94 5.0 2.3 3.3 1.0 versicolor
## 95 5.6 2.7 4.2 1.3 versicolor
## 96 5.7 3.0 4.2 1.2 versicolor
## 97 5.7 2.9 4.2 1.3 versicolor
## 98 6.2 2.9 4.3 1.3 versicolor
## 99 5.1 2.5 3.0 1.1 versicolor
## 100 5.7 2.8 4.1 1.3 versicolor
## 101 6.3 3.3 6.0 2.5 virginica
## 102 5.8 2.7 5.1 1.9 virginica
## 103 7.1 3.0 5.9 2.1 virginica
## 104 6.3 2.9 5.6 1.8 virginica
## 105 6.5 3.0 5.8 2.2 virginica
## 106 7.6 3.0 6.6 2.1 virginica
## 107 4.9 2.5 4.5 1.7 virginica
## 108 7.3 2.9 6.3 1.8 virginica
## 109 6.7 2.5 5.8 1.8 virginica
## 110 7.2 3.6 6.1 2.5 virginica
## 111 6.5 3.2 5.1 2.0 virginica
## 112 6.4 2.7 5.3 1.9 virginica
## 113 6.8 3.0 5.5 2.1 virginica
## 114 5.7 2.5 5.0 2.0 virginica
## 115 5.8 2.8 5.1 2.4 virginica
## 116 6.4 3.2 5.3 2.3 virginica
## 117 6.5 3.0 5.5 1.8 virginica
## 118 7.7 3.8 6.7 2.2 virginica
## 119 7.7 2.6 6.9 2.3 virginica
## 120 6.0 2.2 5.0 1.5 virginica
## 121 6.9 3.2 5.7 2.3 virginica
## 122 5.6 2.8 4.9 2.0 virginica
## 123 7.7 2.8 6.7 2.0 virginica
## 124 6.3 2.7 4.9 1.8 virginica
## 125 6.7 3.3 5.7 2.1 virginica
## 126 7.2 3.2 6.0 1.8 virginica
## 127 6.2 2.8 4.8 1.8 virginica
## 128 6.1 3.0 4.9 1.8 virginica
## 129 6.4 2.8 5.6 2.1 virginica
## 130 7.2 3.0 5.8 1.6 virginica
## 131 7.4 2.8 6.1 1.9 virginica
## 132 7.9 3.8 6.4 2.0 virginica
## 133 6.4 2.8 5.6 2.2 virginica
## 134 6.3 2.8 5.1 1.5 virginica
## 135 6.1 2.6 5.6 1.4 virginica
## 136 7.7 3.0 6.1 2.3 virginica
## 137 6.3 3.4 5.6 2.4 virginica
## 138 6.4 3.1 5.5 1.8 virginica
## 139 6.0 3.0 4.8 1.8 virginica
## 140 6.9 3.1 5.4 2.1 virginica
## 141 6.7 3.1 5.6 2.4 virginica
## 142 6.9 3.1 5.1 2.3 virginica
## 143 5.8 2.7 5.1 1.9 virginica
## 144 6.8 3.2 5.9 2.3 virginica
## 145 6.7 3.3 5.7 2.5 virginica
## 146 6.7 3.0 5.2 2.3 virginica
## 147 6.3 2.5 5.0 1.9 virginica
## 148 6.5 3.0 5.2 2.0 virginica
## 149 6.2 3.4 5.4 2.3 virginica
## 150 5.9 3.0 5.1 1.8 virginicaas_tibble(iris) # shows only a few rows as well as the type of data in each row## # A tibble: 150 × 5
## Sepal.Length Sepal.Width Petal.Length Petal.Width Species
## <dbl> <dbl> <dbl> <dbl> <fctr>
## 1 5.1 3.5 1.4 0.2 setosa
## 2 4.9 3.0 1.4 0.2 setosa
## 3 4.7 3.2 1.3 0.2 setosa
## 4 4.6 3.1 1.5 0.2 setosa
## 5 5.0 3.6 1.4 0.2 setosa
## 6 5.4 3.9 1.7 0.4 setosa
## 7 4.6 3.4 1.4 0.3 setosa
## 8 5.0 3.4 1.5 0.2 setosa
## 9 4.4 2.9 1.4 0.2 setosa
## 10 4.9 3.1 1.5 0.1 setosa
## # ... with 140 more rowsTibbles - Partial Matching
iris$Spec## [1] setosa setosa setosa setosa setosa setosa setosa setosa setosa setosa
## [11] setosa setosa setosa setosa setosa setosa setosa setosa setosa setosa
## [21] setosa setosa setosa setosa setosa setosa setosa setosa setosa setosa
## [31] setosa setosa setosa setosa setosa setosa setosa setosa setosa setosa
## [41] setosa setosa setosa setosa setosa setosa setosa setosa setosa setosa
## [51] versicolor versicolor versicolor versicolor versicolor versicolor versicolor versicolor versicolor versicolor
## [61] versicolor versicolor versicolor versicolor versicolor versicolor versicolor versicolor versicolor versicolor
## [71] versicolor versicolor versicolor versicolor versicolor versicolor versicolor versicolor versicolor versicolor
## [81] versicolor versicolor versicolor versicolor versicolor versicolor versicolor versicolor versicolor versicolor
## [91] versicolor versicolor versicolor versicolor versicolor versicolor versicolor versicolor versicolor versicolor
## [101] virginica virginica virginica virginica virginica virginica virginica virginica virginica virginica
## [111] virginica virginica virginica virginica virginica virginica virginica virginica virginica virginica
## [121] virginica virginica virginica virginica virginica virginica virginica virginica virginica virginica
## [131] virginica virginica virginica virginica virginica virginica virginica virginica virginica virginica
## [141] virginica virginica virginica virginica virginica virginica virginica virginica virginica virginica
## Levels: setosa versicolor virginicaas_tibble(iris)$Spec## Warning: Unknown or uninitialised column: 'Spec'.## NULLTibbles - Subsetting
iris[1]## Sepal.Length
## 1 5.1
## 2 4.9
## 3 4.7
## 4 4.6
## 5 5.0
## 6 5.4
## 7 4.6
## 8 5.0
## 9 4.4
## 10 4.9
## 11 5.4
## 12 4.8
## 13 4.8
## 14 4.3
## 15 5.8
## 16 5.7
## 17 5.4
## 18 5.1
## 19 5.7
## 20 5.1
## 21 5.4
## 22 5.1
## 23 4.6
## 24 5.1
## 25 4.8
## 26 5.0
## 27 5.0
## 28 5.2
## 29 5.2
## 30 4.7
## 31 4.8
## 32 5.4
## 33 5.2
## 34 5.5
## 35 4.9
## 36 5.0
## 37 5.5
## 38 4.9
## 39 4.4
## 40 5.1
## 41 5.0
## 42 4.5
## 43 4.4
## 44 5.0
## 45 5.1
## 46 4.8
## 47 5.1
## 48 4.6
## 49 5.3
## 50 5.0
## 51 7.0
## 52 6.4
## 53 6.9
## 54 5.5
## 55 6.5
## 56 5.7
## 57 6.3
## 58 4.9
## 59 6.6
## 60 5.2
## 61 5.0
## 62 5.9
## 63 6.0
## 64 6.1
## 65 5.6
## 66 6.7
## 67 5.6
## 68 5.8
## 69 6.2
## 70 5.6
## 71 5.9
## 72 6.1
## 73 6.3
## 74 6.1
## 75 6.4
## 76 6.6
## 77 6.8
## 78 6.7
## 79 6.0
## 80 5.7
## 81 5.5
## 82 5.5
## 83 5.8
## 84 6.0
## 85 5.4
## 86 6.0
## 87 6.7
## 88 6.3
## 89 5.6
## 90 5.5
## 91 5.5
## 92 6.1
## 93 5.8
## 94 5.0
## 95 5.6
## 96 5.7
## 97 5.7
## 98 6.2
## 99 5.1
## 100 5.7
## 101 6.3
## 102 5.8
## 103 7.1
## 104 6.3
## 105 6.5
## 106 7.6
## 107 4.9
## 108 7.3
## 109 6.7
## 110 7.2
## 111 6.5
## 112 6.4
## 113 6.8
## 114 5.7
## 115 5.8
## 116 6.4
## 117 6.5
## 118 7.7
## 119 7.7
## 120 6.0
## 121 6.9
## 122 5.6
## 123 7.7
## 124 6.3
## 125 6.7
## 126 7.2
## 127 6.2
## 128 6.1
## 129 6.4
## 130 7.2
## 131 7.4
## 132 7.9
## 133 6.4
## 134 6.3
## 135 6.1
## 136 7.7
## 137 6.3
## 138 6.4
## 139 6.0
## 140 6.9
## 141 6.7
## 142 6.9
## 143 5.8
## 144 6.8
## 145 6.7
## 146 6.7
## 147 6.3
## 148 6.5
## 149 6.2
## 150 5.9iris[, 1]## [1] 5.1 4.9 4.7 4.6 5.0 5.4 4.6 5.0 4.4 4.9 5.4 4.8 4.8 4.3 5.8 5.7 5.4 5.1 5.7 5.1 5.4 5.1 4.6 5.1 4.8 5.0 5.0 5.2
## [29] 5.2 4.7 4.8 5.4 5.2 5.5 4.9 5.0 5.5 4.9 4.4 5.1 5.0 4.5 4.4 5.0 5.1 4.8 5.1 4.6 5.3 5.0 7.0 6.4 6.9 5.5 6.5 5.7
## [57] 6.3 4.9 6.6 5.2 5.0 5.9 6.0 6.1 5.6 6.7 5.6 5.8 6.2 5.6 5.9 6.1 6.3 6.1 6.4 6.6 6.8 6.7 6.0 5.7 5.5 5.5 5.8 6.0
## [85] 5.4 6.0 6.7 6.3 5.6 5.5 5.5 6.1 5.8 5.0 5.6 5.7 5.7 6.2 5.1 5.7 6.3 5.8 7.1 6.3 6.5 7.6 4.9 7.3 6.7 7.2 6.5 6.4
## [113] 6.8 5.7 5.8 6.4 6.5 7.7 7.7 6.0 6.9 5.6 7.7 6.3 6.7 7.2 6.2 6.1 6.4 7.2 7.4 7.9 6.4 6.3 6.1 7.7 6.3 6.4 6.0 6.9
## [141] 6.7 6.9 5.8 6.8 6.7 6.7 6.3 6.5 6.2 5.9as_tibble(iris)[1]## # A tibble: 150 × 1
## Sepal.Length
## <dbl>
## 1 5.1
## 2 4.9
## 3 4.7
## 4 4.6
## 5 5.0
## 6 5.4
## 7 4.6
## 8 5.0
## 9 4.4
## 10 4.9
## # ... with 140 more rowsas_tibble(iris)[, 1]## # A tibble: 150 × 1
## Sepal.Length
## <dbl>
## 1 5.1
## 2 4.9
## 3 4.7
## 4 4.6
## 5 5.0
## 6 5.4
## 7 4.6
## 8 5.0
## 9 4.4
## 10 4.9
## # ... with 140 more rowsas_tibble(iris)[[1]]## [1] 5.1 4.9 4.7 4.6 5.0 5.4 4.6 5.0 4.4 4.9 5.4 4.8 4.8 4.3 5.8 5.7 5.4 5.1 5.7 5.1 5.4 5.1 4.6 5.1 4.8 5.0 5.0 5.2
## [29] 5.2 4.7 4.8 5.4 5.2 5.5 4.9 5.0 5.5 4.9 4.4 5.1 5.0 4.5 4.4 5.0 5.1 4.8 5.1 4.6 5.3 5.0 7.0 6.4 6.9 5.5 6.5 5.7
## [57] 6.3 4.9 6.6 5.2 5.0 5.9 6.0 6.1 5.6 6.7 5.6 5.8 6.2 5.6 5.9 6.1 6.3 6.1 6.4 6.6 6.8 6.7 6.0 5.7 5.5 5.5 5.8 6.0
## [85] 5.4 6.0 6.7 6.3 5.6 5.5 5.5 6.1 5.8 5.0 5.6 5.7 5.7 6.2 5.1 5.7 6.3 5.8 7.1 6.3 6.5 7.6 4.9 7.3 6.7 7.2 6.5 6.4
## [113] 6.8 5.7 5.8 6.4 6.5 7.7 7.7 6.0 6.9 5.6 7.7 6.3 6.7 7.2 6.2 6.1 6.4 7.2 7.4 7.9 6.4 6.3 6.1 7.7 6.3 6.4 6.0 6.9
## [141] 6.7 6.9 5.8 6.8 6.7 6.7 6.3 6.5 6.2 5.9dplyr and the 5 + 1 verbs of data manipulation
dplyr is one of the packages in tidyverse which provides a consistent set of data manipulation verbs.
- filter
- Select based on values
- arrange
- reorder
- select & rename
- select based on names
- mutate & transmute
- add new variables that are functions of existing variables
- summarise
- condense multiple values to a single value
- group by
- perform any operation by group
dplyr syntax
- The structure of the verbs is the same regardless of which one you use
- verb(data frame, variable1/argument1, variable2/argument2, …)
- The result is a new data frame
filter(iris, Sepal.Length > 4, Petal.Width == 0.1) # Note that the variable names do not have quotes, '', around them## Sepal.Length Sepal.Width Petal.Length Petal.Width Species
## 1 4.9 3.1 1.5 0.1 setosa
## 2 4.8 3.0 1.4 0.1 setosa
## 3 4.3 3.0 1.1 0.1 setosa
## 4 5.2 4.1 1.5 0.1 setosa
## 5 4.9 3.6 1.4 0.1 setosaFlights dataset
- On-time data for all flights that departed NYC (i.e. JFK, LGA or EWR) in 2013
- Install the nycflights13 package,
install.packages("nycflights13"), and load its library,library(nycflights13).
library(nycflights13)
flights## # A tibble: 336,776 × 19
## year month day dep_time sched_dep_time dep_delay arr_time sched_arr_time arr_delay carrier flight tailnum origin
## <int> <int> <int> <int> <int> <dbl> <int> <int> <dbl> <chr> <int> <chr> <chr>
## 1 2013 1 1 517 515 2 830 819 11 UA 1545 N14228 EWR
## 2 2013 1 1 533 529 4 850 830 20 UA 1714 N24211 LGA
## 3 2013 1 1 542 540 2 923 850 33 AA 1141 N619AA JFK
## 4 2013 1 1 544 545 -1 1004 1022 -18 B6 725 N804JB JFK
## 5 2013 1 1 554 600 -6 812 837 -25 DL 461 N668DN LGA
## 6 2013 1 1 554 558 -4 740 728 12 UA 1696 N39463 EWR
## 7 2013 1 1 555 600 -5 913 854 19 B6 507 N516JB EWR
## 8 2013 1 1 557 600 -3 709 723 -14 EV 5708 N829AS LGA
## 9 2013 1 1 557 600 -3 838 846 -8 B6 79 N593JB JFK
## 10 2013 1 1 558 600 -2 753 745 8 AA 301 N3ALAA LGA
## # ... with 336,766 more rows, and 6 more variables: dest <chr>, air_time <dbl>, distance <dbl>, hour <dbl>,
## # minute <dbl>, time_hour <dttm>summary(flights)## year month day dep_time sched_dep_time dep_delay arr_time
## Min. :2013 Min. : 1.000 Min. : 1.00 Min. : 1 Min. : 106 Min. : -43.00 Min. : 1
## 1st Qu.:2013 1st Qu.: 4.000 1st Qu.: 8.00 1st Qu.: 907 1st Qu.: 906 1st Qu.: -5.00 1st Qu.:1104
## Median :2013 Median : 7.000 Median :16.00 Median :1401 Median :1359 Median : -2.00 Median :1535
## Mean :2013 Mean : 6.549 Mean :15.71 Mean :1349 Mean :1344 Mean : 12.64 Mean :1502
## 3rd Qu.:2013 3rd Qu.:10.000 3rd Qu.:23.00 3rd Qu.:1744 3rd Qu.:1729 3rd Qu.: 11.00 3rd Qu.:1940
## Max. :2013 Max. :12.000 Max. :31.00 Max. :2400 Max. :2359 Max. :1301.00 Max. :2400
## NA's :8255 NA's :8255 NA's :8713
## sched_arr_time arr_delay carrier flight tailnum origin
## Min. : 1 Min. : -86.000 Length:336776 Min. : 1 Length:336776 Length:336776
## 1st Qu.:1124 1st Qu.: -17.000 Class :character 1st Qu.: 553 Class :character Class :character
## Median :1556 Median : -5.000 Mode :character Median :1496 Mode :character Mode :character
## Mean :1536 Mean : 6.895 Mean :1972
## 3rd Qu.:1945 3rd Qu.: 14.000 3rd Qu.:3465
## Max. :2359 Max. :1272.000 Max. :8500
## NA's :9430
## dest air_time distance hour minute time_hour
## Length:336776 Min. : 20.0 Min. : 17 Min. : 1.00 Min. : 0.00 Min. :2013-01-01 05:00:00
## Class :character 1st Qu.: 82.0 1st Qu.: 502 1st Qu.: 9.00 1st Qu.: 8.00 1st Qu.:2013-04-04 13:00:00
## Mode :character Median :129.0 Median : 872 Median :13.00 Median :29.00 Median :2013-07-03 10:00:00
## Mean :150.7 Mean :1040 Mean :13.18 Mean :26.23 Mean :2013-07-03 05:02:36
## 3rd Qu.:192.0 3rd Qu.:1389 3rd Qu.:17.00 3rd Qu.:44.00 3rd Qu.:2013-10-01 07:00:00
## Max. :695.0 Max. :4983 Max. :23.00 Max. :59.00 Max. :2013-12-31 23:00:00
## NA's :9430Data Types
intintegersdbldoubles or real numberschrcharacter vectors (strings)dttmdate-timedatedatelgllogical (TRUE or FALSE)fctrfactors (catgeorical variables with fixed possible values, e.g., dropdown list)listlike a vector but can contain different types of elements
flights[c("dep_time", "tailnum", "air_time", "time_hour")]## # A tibble: 336,776 × 4
## dep_time tailnum air_time time_hour
## <int> <chr> <dbl> <dttm>
## 1 517 N14228 227 2013-01-01 05:00:00
## 2 533 N24211 227 2013-01-01 05:00:00
## 3 542 N619AA 160 2013-01-01 05:00:00
## 4 544 N804JB 183 2013-01-01 05:00:00
## 5 554 N668DN 116 2013-01-01 06:00:00
## 6 554 N39463 150 2013-01-01 05:00:00
## 7 555 N516JB 158 2013-01-01 06:00:00
## 8 557 N829AS 53 2013-01-01 06:00:00
## 9 557 N593JB 140 2013-01-01 06:00:00
## 10 558 N3ALAA 138 2013-01-01 06:00:00
## # ... with 336,766 more rowsfilter
use filter() to find rows/cases where conditions are true
# Find all flights which went from JFK to Fort Lauderdale in the first week of January
filter(flights, origin == "JFK", dest == "FLL", month == 1, day <= 7)## # A tibble: 106 × 19
## year month day dep_time sched_dep_time dep_delay arr_time sched_arr_time arr_delay carrier flight tailnum origin
## <int> <int> <int> <int> <int> <dbl> <int> <int> <dbl> <chr> <int> <chr> <chr>
## 1 2013 1 1 659 700 -1 1008 1007 1 B6 981 N646JB JFK
## 2 2013 1 1 712 715 -3 1023 1035 -12 AA 825 N3ETAA JFK
## 3 2013 1 1 805 800 5 1118 1106 12 B6 3 N570JB JFK
## 4 2013 1 1 933 904 29 1252 1210 42 B6 17 N579JB JFK
## 5 2013 1 1 1153 1123 30 1454 1425 29 B6 1 N552JB JFK
## 6 2013 1 1 1251 1252 -1 1611 1555 16 B6 85 N657JB JFK
## 7 2013 1 1 1452 1457 -5 1753 1811 -18 B6 61 N292JB JFK
## 8 2013 1 1 1527 1530 -3 1841 1855 -14 AA 1039 N3HYAA JFK
## 9 2013 1 1 1610 1615 -5 1913 1948 -35 DL 1411 N947DL JFK
## 10 2013 1 1 1713 1700 13 2006 2014 -8 B6 15 N346JB JFK
## # ... with 96 more rows, and 6 more variables: dest <chr>, air_time <dbl>, distance <dbl>, hour <dbl>, minute <dbl>,
## # time_hour <dttm>filter(flights, (origin == "JFK" | dest == "FLL"), month == 1, day <= 7) # , is the same as AND and | is the same as OR## # A tibble: 2,340 × 19
## year month day dep_time sched_dep_time dep_delay arr_time sched_arr_time arr_delay carrier flight tailnum origin
## <int> <int> <int> <int> <int> <dbl> <int> <int> <dbl> <chr> <int> <chr> <chr>
## 1 2013 1 1 542 540 2 923 850 33 AA 1141 N619AA JFK
## 2 2013 1 1 544 545 -1 1004 1022 -18 B6 725 N804JB JFK
## 3 2013 1 1 555 600 -5 913 854 19 B6 507 N516JB EWR
## 4 2013 1 1 557 600 -3 838 846 -8 B6 79 N593JB JFK
## 5 2013 1 1 558 600 -2 849 851 -2 B6 49 N793JB JFK
## 6 2013 1 1 558 600 -2 853 856 -3 B6 71 N657JB JFK
## 7 2013 1 1 558 600 -2 924 917 7 UA 194 N29129 JFK
## 8 2013 1 1 559 559 0 702 706 -4 B6 1806 N708JB JFK
## 9 2013 1 1 600 600 0 851 858 -7 B6 371 N595JB LGA
## 10 2013 1 1 606 610 -4 837 845 -8 DL 1743 N3739P JFK
## # ... with 2,330 more rows, and 6 more variables: dest <chr>, air_time <dbl>, distance <dbl>, hour <dbl>, minute <dbl>,
## # time_hour <dttm># Find all flights going to Fort Lauderdale, Atlanta or O'Hare
filter(flights, dest == "FLL" | dest == "ATL" | dest == "ORD")## # A tibble: 46,553 × 19
## year month day dep_time sched_dep_time dep_delay arr_time sched_arr_time arr_delay carrier flight tailnum origin
## <int> <int> <int> <int> <int> <dbl> <int> <int> <dbl> <chr> <int> <chr> <chr>
## 1 2013 1 1 554 600 -6 812 837 -25 DL 461 N668DN LGA
## 2 2013 1 1 554 558 -4 740 728 12 UA 1696 N39463 EWR
## 3 2013 1 1 555 600 -5 913 854 19 B6 507 N516JB EWR
## 4 2013 1 1 558 600 -2 753 745 8 AA 301 N3ALAA LGA
## 5 2013 1 1 600 600 0 851 858 -7 B6 371 N595JB LGA
## 6 2013 1 1 600 600 0 837 825 12 MQ 4650 N542MQ LGA
## 7 2013 1 1 606 610 -4 837 845 -8 DL 1743 N3739P JFK
## 8 2013 1 1 608 600 8 807 735 32 MQ 3768 N9EAMQ EWR
## 9 2013 1 1 615 615 0 833 842 -9 DL 575 N326NB EWR
## 10 2013 1 1 629 630 -1 824 810 14 AA 303 N3CYAA LGA
## # ... with 46,543 more rows, and 6 more variables: dest <chr>, air_time <dbl>, distance <dbl>, hour <dbl>,
## # minute <dbl>, time_hour <dttm>filter(flights, dest %in% c("FLL", "ATL", "ORD")) # use %in% to search for multiple values in a single variable## # A tibble: 46,553 × 19
## year month day dep_time sched_dep_time dep_delay arr_time sched_arr_time arr_delay carrier flight tailnum origin
## <int> <int> <int> <int> <int> <dbl> <int> <int> <dbl> <chr> <int> <chr> <chr>
## 1 2013 1 1 554 600 -6 812 837 -25 DL 461 N668DN LGA
## 2 2013 1 1 554 558 -4 740 728 12 UA 1696 N39463 EWR
## 3 2013 1 1 555 600 -5 913 854 19 B6 507 N516JB EWR
## 4 2013 1 1 558 600 -2 753 745 8 AA 301 N3ALAA LGA
## 5 2013 1 1 600 600 0 851 858 -7 B6 371 N595JB LGA
## 6 2013 1 1 600 600 0 837 825 12 MQ 4650 N542MQ LGA
## 7 2013 1 1 606 610 -4 837 845 -8 DL 1743 N3739P JFK
## 8 2013 1 1 608 600 8 807 735 32 MQ 3768 N9EAMQ EWR
## 9 2013 1 1 615 615 0 833 842 -9 DL 575 N326NB EWR
## 10 2013 1 1 629 630 -1 824 810 14 AA 303 N3CYAA LGA
## # ... with 46,543 more rows, and 6 more variables: dest <chr>, air_time <dbl>, distance <dbl>, hour <dbl>,
## # minute <dbl>, time_hour <dttm># Find all flights that have values for their departure delays
filter(flights, is.na(dep_delay)) # show all the rows with NA (missing values)## # A tibble: 8,255 × 19
## year month day dep_time sched_dep_time dep_delay arr_time sched_arr_time arr_delay carrier flight tailnum origin
## <int> <int> <int> <int> <int> <dbl> <int> <int> <dbl> <chr> <int> <chr> <chr>
## 1 2013 1 1 NA 1630 NA NA 1815 NA EV 4308 N18120 EWR
## 2 2013 1 1 NA 1935 NA NA 2240 NA AA 791 N3EHAA LGA
## 3 2013 1 1 NA 1500 NA NA 1825 NA AA 1925 N3EVAA LGA
## 4 2013 1 1 NA 600 NA NA 901 NA B6 125 N618JB JFK
## 5 2013 1 2 NA 1540 NA NA 1747 NA EV 4352 N10575 EWR
## 6 2013 1 2 NA 1620 NA NA 1746 NA EV 4406 N13949 EWR
## 7 2013 1 2 NA 1355 NA NA 1459 NA EV 4434 N10575 EWR
## 8 2013 1 2 NA 1420 NA NA 1644 NA EV 4935 N759EV EWR
## 9 2013 1 2 NA 1321 NA NA 1536 NA EV 3849 N13550 EWR
## 10 2013 1 2 NA 1545 NA NA 1910 NA AA 133 <NA> JFK
## # ... with 8,245 more rows, and 6 more variables: dest <chr>, air_time <dbl>, distance <dbl>, hour <dbl>, minute <dbl>,
## # time_hour <dttm>filter(flights, !is.na(dep_delay)) # show only the rows without missing values## # A tibble: 328,521 × 19
## year month day dep_time sched_dep_time dep_delay arr_time sched_arr_time arr_delay carrier flight tailnum origin
## <int> <int> <int> <int> <int> <dbl> <int> <int> <dbl> <chr> <int> <chr> <chr>
## 1 2013 1 1 517 515 2 830 819 11 UA 1545 N14228 EWR
## 2 2013 1 1 533 529 4 850 830 20 UA 1714 N24211 LGA
## 3 2013 1 1 542 540 2 923 850 33 AA 1141 N619AA JFK
## 4 2013 1 1 544 545 -1 1004 1022 -18 B6 725 N804JB JFK
## 5 2013 1 1 554 600 -6 812 837 -25 DL 461 N668DN LGA
## 6 2013 1 1 554 558 -4 740 728 12 UA 1696 N39463 EWR
## 7 2013 1 1 555 600 -5 913 854 19 B6 507 N516JB EWR
## 8 2013 1 1 557 600 -3 709 723 -14 EV 5708 N829AS LGA
## 9 2013 1 1 557 600 -3 838 846 -8 B6 79 N593JB JFK
## 10 2013 1 1 558 600 -2 753 745 8 AA 301 N3ALAA LGA
## # ... with 328,511 more rows, and 6 more variables: dest <chr>, air_time <dbl>, distance <dbl>, hour <dbl>,
## # minute <dbl>, time_hour <dttm>arrange
use arrange() to sort the data based on one or more variables
# Sort the flights based on their scheduled departure time
arrange(flights, sched_dep_time)## # A tibble: 336,776 × 19
## year month day dep_time sched_dep_time dep_delay arr_time sched_arr_time arr_delay carrier flight tailnum origin
## <int> <int> <int> <int> <int> <dbl> <int> <int> <dbl> <chr> <int> <chr> <chr>
## 1 2013 7 27 NA 106 NA NA 245 NA US 1632 <NA> EWR
## 2 2013 1 2 458 500 -2 703 650 13 US 1030 N162UW EWR
## 3 2013 1 3 458 500 -2 650 650 0 US 1030 N172US EWR
## 4 2013 1 4 456 500 -4 631 650 -19 US 1030 N186US EWR
## 5 2013 1 5 458 500 -2 640 650 -10 US 1030 N560UW EWR
## 6 2013 1 6 458 500 -2 718 650 28 US 1030 N539UW EWR
## 7 2013 1 7 454 500 -6 637 648 -11 US 1117 N566UW EWR
## 8 2013 1 8 454 500 -6 625 648 -23 US 1117 N564UW EWR
## 9 2013 1 9 457 500 -3 647 648 -1 US 1117 N566UW EWR
## 10 2013 1 10 450 500 -10 634 648 -14 US 1117 N171US EWR
## # ... with 336,766 more rows, and 6 more variables: dest <chr>, air_time <dbl>, distance <dbl>, hour <dbl>,
## # minute <dbl>, time_hour <dttm># Sort the flights based on their scheduled departure time, and break ties using their actual departure time
arrange(flights, sched_dep_time, dep_time)## # A tibble: 336,776 × 19
## year month day dep_time sched_dep_time dep_delay arr_time sched_arr_time arr_delay carrier flight tailnum origin
## <int> <int> <int> <int> <int> <dbl> <int> <int> <dbl> <chr> <int> <chr> <chr>
## 1 2013 7 27 NA 106 NA NA 245 NA US 1632 <NA> EWR
## 2 2013 5 8 445 500 -15 620 640 -20 US 1431 N537UW EWR
## 3 2013 5 5 446 500 -14 636 640 -4 US 1579 N768US EWR
## 4 2013 9 4 446 500 -14 618 648 -30 US 1877 N567UW EWR
## 5 2013 10 1 447 500 -13 614 648 -34 US 1877 N538UW EWR
## 6 2013 9 19 447 500 -13 620 648 -28 US 1877 N199UW EWR
## 7 2013 1 29 448 500 -12 635 648 -13 US 1117 N172US EWR
## 8 2013 12 27 448 500 -12 648 651 -3 US 1895 N543UW EWR
## 9 2013 5 7 448 500 -12 624 640 -16 US 1099 N565UW EWR
## 10 2013 10 2 449 500 -11 620 648 -28 US 1877 N193UW EWR
## # ... with 336,766 more rows, and 6 more variables: dest <chr>, air_time <dbl>, distance <dbl>, hour <dbl>,
## # minute <dbl>, time_hour <dttm># Sort the flights by those scheduled to depart latest, and break ties in that group by those who left earliest
arrange(flights, desc(sched_dep_time), dep_time)## # A tibble: 336,776 × 19
## year month day dep_time sched_dep_time dep_delay arr_time sched_arr_time arr_delay carrier flight tailnum origin
## <int> <int> <int> <int> <int> <dbl> <int> <int> <dbl> <chr> <int> <chr> <chr>
## 1 2013 11 13 1 2359 2 442 440 2 B6 1503 N627JB JFK
## 2 2013 12 16 1 2359 2 447 437 10 B6 839 N607JB JFK
## 3 2013 12 20 1 2359 2 430 440 -10 B6 1503 N608JB JFK
## 4 2013 12 26 1 2359 2 437 440 -3 B6 1503 N527JB JFK
## 5 2013 12 30 1 2359 2 441 437 4 B6 839 N508JB JFK
## 6 2013 4 5 1 2359 2 410 339 31 B6 727 N606JB JFK
## 7 2013 5 25 1 2359 2 336 341 -5 B6 727 N523JB JFK
## 8 2013 6 20 1 2359 2 340 350 -10 B6 745 N517JB JFK
## 9 2013 7 27 1 2359 2 345 340 5 B6 839 N503JB JFK
## 10 2013 7 28 1 2359 2 423 350 33 B6 745 N703JB JFK
## # ... with 336,766 more rows, and 6 more variables: dest <chr>, air_time <dbl>, distance <dbl>, hour <dbl>,
## # minute <dbl>, time_hour <dttm>- The problems is I forgot about flights which were delayed so left the next morning
- Since dep_time is day agnostic, this does not give me the data I am looking for
- I can try and figure out which flights left that day and which left the next or just use a different variable as my metric of the late evening flights which left earliest.
arrange(flights, desc(sched_dep_time), dep_delay)## # A tibble: 336,776 × 19
## year month day dep_time sched_dep_time dep_delay arr_time sched_arr_time arr_delay carrier flight tailnum origin
## <int> <int> <int> <int> <int> <dbl> <int> <int> <dbl> <chr> <int> <chr> <chr>
## 1 2013 10 2 2341 2359 -18 324 350 -26 B6 745 N527JB JFK
## 2 2013 9 23 2342 2359 -17 331 350 -19 B6 745 N503JB JFK
## 3 2013 10 22 2343 2359 -16 347 350 -3 B6 745 N592JB JFK
## 4 2013 3 4 2343 2359 -16 418 438 -20 B6 727 N603JB JFK
## 5 2013 1 20 2344 2359 -15 428 437 -9 B6 727 N603JB JFK
## 6 2013 4 16 2344 2359 -15 313 343 -30 B6 707 N554JB JFK
## 7 2013 1 27 2345 2359 -14 424 444 -20 B6 739 N630JB JFK
## 8 2013 3 3 2345 2359 -14 441 438 3 B6 727 N508JB JFK
## 9 2013 3 5 2345 2359 -14 439 438 1 B6 727 N705JB JFK
## 10 2013 10 6 2346 2359 -13 333 350 -17 B6 745 N636JB JFK
## # ... with 336,766 more rows, and 6 more variables: dest <chr>, air_time <dbl>, distance <dbl>, hour <dbl>,
## # minute <dbl>, time_hour <dttm>select & rename
use select() and rename() to pick variables based on their names
# Select the year, month, day, dep_times, and sched_dep_time columns
select(flights, year, month, day, dep_time, sched_dep_time)## # A tibble: 336,776 × 5
## year month day dep_time sched_dep_time
## <int> <int> <int> <int> <int>
## 1 2013 1 1 517 515
## 2 2013 1 1 533 529
## 3 2013 1 1 542 540
## 4 2013 1 1 544 545
## 5 2013 1 1 554 600
## 6 2013 1 1 554 558
## 7 2013 1 1 555 600
## 8 2013 1 1 557 600
## 9 2013 1 1 557 600
## 10 2013 1 1 558 600
## # ... with 336,766 more rowsselect(flights, year:sched_dep_time)## # A tibble: 336,776 × 5
## year month day dep_time sched_dep_time
## <int> <int> <int> <int> <int>
## 1 2013 1 1 517 515
## 2 2013 1 1 533 529
## 3 2013 1 1 542 540
## 4 2013 1 1 544 545
## 5 2013 1 1 554 600
## 6 2013 1 1 554 558
## 7 2013 1 1 555 600
## 8 2013 1 1 557 600
## 9 2013 1 1 557 600
## 10 2013 1 1 558 600
## # ... with 336,766 more rowsselect(flights, 1:5)## # A tibble: 336,776 × 5
## year month day dep_time sched_dep_time
## <int> <int> <int> <int> <int>
## 1 2013 1 1 517 515
## 2 2013 1 1 533 529
## 3 2013 1 1 542 540
## 4 2013 1 1 544 545
## 5 2013 1 1 554 600
## 6 2013 1 1 554 558
## 7 2013 1 1 555 600
## 8 2013 1 1 557 600
## 9 2013 1 1 557 600
## 10 2013 1 1 558 600
## # ... with 336,766 more rowsselect(flights, -(dep_delay:time_hour)) # more useful when removing only a few columns## # A tibble: 336,776 × 5
## year month day dep_time sched_dep_time
## <int> <int> <int> <int> <int>
## 1 2013 1 1 517 515
## 2 2013 1 1 533 529
## 3 2013 1 1 542 540
## 4 2013 1 1 544 545
## 5 2013 1 1 554 600
## 6 2013 1 1 554 558
## 7 2013 1 1 555 600
## 8 2013 1 1 557 600
## 9 2013 1 1 557 600
## 10 2013 1 1 558 600
## # ... with 336,766 more rowsrename lets you change the name of a variable while still keeping the full data set
rename(flights, sun_cycles = year)## # A tibble: 336,776 × 19
## sun_cycles month day dep_time sched_dep_time dep_delay arr_time sched_arr_time arr_delay carrier flight tailnum
## <int> <int> <int> <int> <int> <dbl> <int> <int> <dbl> <chr> <int> <chr>
## 1 2013 1 1 517 515 2 830 819 11 UA 1545 N14228
## 2 2013 1 1 533 529 4 850 830 20 UA 1714 N24211
## 3 2013 1 1 542 540 2 923 850 33 AA 1141 N619AA
## 4 2013 1 1 544 545 -1 1004 1022 -18 B6 725 N804JB
## 5 2013 1 1 554 600 -6 812 837 -25 DL 461 N668DN
## 6 2013 1 1 554 558 -4 740 728 12 UA 1696 N39463
## 7 2013 1 1 555 600 -5 913 854 19 B6 507 N516JB
## 8 2013 1 1 557 600 -3 709 723 -14 EV 5708 N829AS
## 9 2013 1 1 557 600 -3 838 846 -8 B6 79 N593JB
## 10 2013 1 1 558 600 -2 753 745 8 AA 301 N3ALAA
## # ... with 336,766 more rows, and 7 more variables: origin <chr>, dest <chr>, air_time <dbl>, distance <dbl>,
## # hour <dbl>, minute <dbl>, time_hour <dttm>flights # Note that we are not assigning any of these outputs, so if you call the original dataset, it hasn't changed## # A tibble: 336,776 × 19
## year month day dep_time sched_dep_time dep_delay arr_time sched_arr_time arr_delay carrier flight tailnum origin
## <int> <int> <int> <int> <int> <dbl> <int> <int> <dbl> <chr> <int> <chr> <chr>
## 1 2013 1 1 517 515 2 830 819 11 UA 1545 N14228 EWR
## 2 2013 1 1 533 529 4 850 830 20 UA 1714 N24211 LGA
## 3 2013 1 1 542 540 2 923 850 33 AA 1141 N619AA JFK
## 4 2013 1 1 544 545 -1 1004 1022 -18 B6 725 N804JB JFK
## 5 2013 1 1 554 600 -6 812 837 -25 DL 461 N668DN LGA
## 6 2013 1 1 554 558 -4 740 728 12 UA 1696 N39463 EWR
## 7 2013 1 1 555 600 -5 913 854 19 B6 507 N516JB EWR
## 8 2013 1 1 557 600 -3 709 723 -14 EV 5708 N829AS LGA
## 9 2013 1 1 557 600 -3 838 846 -8 B6 79 N593JB JFK
## 10 2013 1 1 558 600 -2 753 745 8 AA 301 N3ALAA LGA
## # ... with 336,766 more rows, and 6 more variables: dest <chr>, air_time <dbl>, distance <dbl>, hour <dbl>,
## # minute <dbl>, time_hour <dttm>The everything() helper lets you use select to rearrange the order of the variables
select(flights, distance, air_time, everything())## # A tibble: 336,776 × 19
## distance air_time year month day dep_time sched_dep_time dep_delay arr_time sched_arr_time arr_delay carrier
## <dbl> <dbl> <int> <int> <int> <int> <int> <dbl> <int> <int> <dbl> <chr>
## 1 1400 227 2013 1 1 517 515 2 830 819 11 UA
## 2 1416 227 2013 1 1 533 529 4 850 830 20 UA
## 3 1089 160 2013 1 1 542 540 2 923 850 33 AA
## 4 1576 183 2013 1 1 544 545 -1 1004 1022 -18 B6
## 5 762 116 2013 1 1 554 600 -6 812 837 -25 DL
## 6 719 150 2013 1 1 554 558 -4 740 728 12 UA
## 7 1065 158 2013 1 1 555 600 -5 913 854 19 B6
## 8 229 53 2013 1 1 557 600 -3 709 723 -14 EV
## 9 944 140 2013 1 1 557 600 -3 838 846 -8 B6
## 10 733 138 2013 1 1 558 600 -2 753 745 8 AA
## # ... with 336,766 more rows, and 7 more variables: flight <int>, tailnum <chr>, origin <chr>, dest <chr>, hour <dbl>,
## # minute <dbl>, time_hour <dttm>mutate & transmute
mutate adds new variables, while transmute drops existing variables
# create a subset of the full dataset so that you can see new variables being added
flights_sml <- select(flights, dep_time, arr_time, air_time, distance)
flights_sml## # A tibble: 336,776 × 4
## dep_time arr_time air_time distance
## <int> <int> <dbl> <dbl>
## 1 517 830 227 1400
## 2 533 850 227 1416
## 3 542 923 160 1089
## 4 544 1004 183 1576
## 5 554 812 116 762
## 6 554 740 150 719
## 7 555 913 158 1065
## 8 557 709 53 229
## 9 557 838 140 944
## 10 558 753 138 733
## # ... with 336,766 more rowsmutate(flights_sml, avg_speed = distance/air_time, dep_hr = dep_time%/%100, dep_min = dep_time%%100)## # A tibble: 336,776 × 7
## dep_time arr_time air_time distance avg_speed dep_hr dep_min
## <int> <int> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 517 830 227 1400 6.167401 5 17
## 2 533 850 227 1416 6.237885 5 33
## 3 542 923 160 1089 6.806250 5 42
## 4 544 1004 183 1576 8.612022 5 44
## 5 554 812 116 762 6.568966 5 54
## 6 554 740 150 719 4.793333 5 54
## 7 555 913 158 1065 6.740506 5 55
## 8 557 709 53 229 4.320755 5 57
## 9 557 838 140 944 6.742857 5 57
## 10 558 753 138 733 5.311594 5 58
## # ... with 336,766 more rowstransmute(flights_sml, avg_speed = distance/air_time, dep_hr = dep_time%/%100, dep_min = dep_time%%100)## # A tibble: 336,776 × 3
## avg_speed dep_hr dep_min
## <dbl> <dbl> <dbl>
## 1 6.167401 5 17
## 2 6.237885 5 33
## 3 6.806250 5 42
## 4 8.612022 5 44
## 5 6.568966 5 54
## 6 4.793333 5 54
## 7 6.740506 5 55
## 8 4.320755 5 57
## 9 6.742857 5 57
## 10 5.311594 5 58
## # ... with 336,766 more rows- There are lots of useful functions which can be applied within mutate/transmute, use
?mutatefor the full suggested listlead()andlag()find the next and previous values in a vector, respectively.
cumsum(),cummean(), and others (see help doc) take running sums, means and other properties
# How much time is there between each flight and the next?
mutate(flights_sml, dep_time_offset = lag(dep_time), dep_time_lag = dep_time - lag(dep_time))## # A tibble: 336,776 × 6
## dep_time arr_time air_time distance dep_time_offset dep_time_lag
## <int> <int> <dbl> <dbl> <int> <int>
## 1 517 830 227 1400 NA NA
## 2 533 850 227 1416 517 16
## 3 542 923 160 1089 533 9
## 4 544 1004 183 1576 542 2
## 5 554 812 116 762 544 10
## 6 554 740 150 719 554 0
## 7 555 913 158 1065 554 1
## 8 557 709 53 229 555 2
## 9 557 838 140 944 557 0
## 10 558 753 138 733 557 1
## # ... with 336,766 more rowsmutate(flights_sml, dep_time_offset = lead(dep_time), dep_time_lead = lead(dep_time) - dep_time)## # A tibble: 336,776 × 6
## dep_time arr_time air_time distance dep_time_offset dep_time_lead
## <int> <int> <dbl> <dbl> <int> <int>
## 1 517 830 227 1400 533 16
## 2 533 850 227 1416 542 9
## 3 542 923 160 1089 544 2
## 4 544 1004 183 1576 554 10
## 5 554 812 116 762 554 0
## 6 554 740 150 719 555 1
## 7 555 913 158 1065 557 2
## 8 557 709 53 229 557 0
## 9 557 838 140 944 558 1
## 10 558 753 138 733 558 0
## # ... with 336,766 more rowsmutate(flights_sml, total_dist = cumsum(distance))## # A tibble: 336,776 × 5
## dep_time arr_time air_time distance total_dist
## <int> <int> <dbl> <dbl> <dbl>
## 1 517 830 227 1400 1400
## 2 533 850 227 1416 2816
## 3 542 923 160 1089 3905
## 4 544 1004 183 1576 5481
## 5 554 812 116 762 6243
## 6 554 740 150 719 6962
## 7 555 913 158 1065 8027
## 8 557 709 53 229 8256
## 9 557 838 140 944 9200
## 10 558 753 138 733 9933
## # ... with 336,766 more rowsSummarise & Group by
Summarise reduces multiple values to a single summary metric
summarise(flights, delay = mean(dep_delay))## # A tibble: 1 × 1
## delay
## <dbl>
## 1 NA- Why does this give us
NA? - In R, missing values are represented by the symbol
NA(not available)- This is not to be confused with
NaN(not a number), which refers to impossible values, e.g., dividing by zero
- This is not to be confused with
- When you try to do any operation that includes
NAvalues, the output will always beNA- Think of
NA’s as being any possible value, as a result any summary metric will result in an unknown quantity as the uknownNAvalue could have significantly impacted the results
- Think of
- To solve this problem most R functions have the option to ignore
NAvalue- Usually it is of the form
na.rm=TRUE
- Usually it is of the form
summarise(flights, delay = mean(dep_delay, na.rm = TRUE))## # A tibble: 1 × 1
## delay
## <dbl>
## 1 12.63907- By itself
summariseisn’t that useful as we rarely want to reduce all our data down to a single metric summariseis much more useful when combined with the other expressions- For example, determining the average departure delay of all flights in January
jan_delay <- filter(flights, month == 1)
summarise(jan_delay, delay = mean(dep_delay, na.rm = TRUE))## # A tibble: 1 × 1
## delay
## <dbl>
## 1 10.03667- However, the real power of
summariseis seen when coupled withgroup_by group_bytakes an existing tibble and converts it into a grouped tibble where operations are performed “by group”- By itself
group_bydoes not change how the data looks, instead it changes how it interacts with the other verbs, most notablysummarise
- By itself
flights_month <- group_by(flights, month)
flights_month## Source: local data frame [336,776 x 19]
## Groups: month [12]
##
## year month day dep_time sched_dep_time dep_delay arr_time sched_arr_time arr_delay carrier flight tailnum origin
## <int> <int> <int> <int> <int> <dbl> <int> <int> <dbl> <chr> <int> <chr> <chr>
## 1 2013 1 1 517 515 2 830 819 11 UA 1545 N14228 EWR
## 2 2013 1 1 533 529 4 850 830 20 UA 1714 N24211 LGA
## 3 2013 1 1 542 540 2 923 850 33 AA 1141 N619AA JFK
## 4 2013 1 1 544 545 -1 1004 1022 -18 B6 725 N804JB JFK
## 5 2013 1 1 554 600 -6 812 837 -25 DL 461 N668DN LGA
## 6 2013 1 1 554 558 -4 740 728 12 UA 1696 N39463 EWR
## 7 2013 1 1 555 600 -5 913 854 19 B6 507 N516JB EWR
## 8 2013 1 1 557 600 -3 709 723 -14 EV 5708 N829AS LGA
## 9 2013 1 1 557 600 -3 838 846 -8 B6 79 N593JB JFK
## 10 2013 1 1 558 600 -2 753 745 8 AA 301 N3ALAA LGA
## # ... with 336,766 more rows, and 6 more variables: dest <chr>, air_time <dbl>, distance <dbl>, hour <dbl>,
## # minute <dbl>, time_hour <dttm>summarise(flights_month, delay = mean(dep_delay, na.rm = TRUE))## # A tibble: 12 × 2
## month delay
## <int> <dbl>
## 1 1 10.036665
## 2 2 10.816843
## 3 3 13.227076
## 4 4 13.938038
## 5 5 12.986859
## 6 6 20.846332
## 7 7 21.727787
## 8 8 12.611040
## 9 9 6.722476
## 10 10 6.243988
## 11 11 5.435362
## 12 12 16.576688Also it’s good practice when grouping to add a counts column using n()
summarise(flights_month, delay = mean(dep_delay, na.rm = TRUE), count = n())## # A tibble: 12 × 3
## month delay count
## <int> <dbl> <int>
## 1 1 10.036665 27004
## 2 2 10.816843 24951
## 3 3 13.227076 28834
## 4 4 13.938038 28330
## 5 5 12.986859 28796
## 6 6 20.846332 28243
## 7 7 21.727787 29425
## 8 8 12.611040 29327
## 9 9 6.722476 27574
## 10 10 6.243988 28889
## 11 11 5.435362 27268
## 12 12 16.576688 28135Pipes
Pipes
Often you will need to string multiple actions together which can get somewhat messy
# On average which hour of the day has the most delayed american airline flights
flights_mut <- mutate(flights, hr = sched_dep_time%/%100)
flights_filt <- filter(flights_mut, carrier == "AA", complete.cases(flights_mut))
flights_sel <- select(flights_filt, dep_time, hr, sched_dep_time, dep_delay)
flights_sel # print out to confirm that you are selecting what you intend## # A tibble: 31,947 × 4
## dep_time hr sched_dep_time dep_delay
## <int> <dbl> <int> <dbl>
## 1 542 5 540 2
## 2 558 6 600 -2
## 3 559 6 600 -1
## 4 606 6 610 -4
## 5 623 6 610 13
## 6 628 6 630 -2
## 7 629 6 630 -1
## 8 635 6 635 0
## 9 656 7 700 -4
## 10 656 6 659 -3
## # ... with 31,937 more rowsflights_gb <- group_by(flights_sel, hr)
flights_sum <- summarise(flights_gb, mean_delay = mean(dep_delay), count = n())
flights_arr <- arrange(flights_sum, desc(mean_delay))
print(flights_arr, n = 24)## # A tibble: 17 × 3
## hr mean_delay count
## <dbl> <dbl> <int>
## 1 19 21.2870418 1937
## 2 17 19.9348861 3993
## 3 21 18.2857143 406
## 4 18 14.3431713 1728
## 5 15 12.3666921 2618
## 6 20 12.2851240 484
## 7 16 11.9728287 2061
## 8 14 7.7936709 1580
## 9 13 7.3642305 1683
## 10 10 5.8927536 1380
## 11 11 5.1475167 1349
## 12 12 4.9592920 2260
## 13 9 2.6576763 2410
## 14 8 2.1545312 1909
## 15 5 0.6814404 361
## 16 7 -0.4511713 3287
## 17 6 -1.0215914 2501The pipes %>% or CTRL+Shift+M (from the magrittr package which is included in tidyverse) allows you to do the same set of actions in a much simpler manner
flights %>%
mutate(hr = sched_dep_time%/% 100) %>%
filter(carrier == 'AA', complete.cases(flights_mut)) %>%
select(dep_time, hr, sched_dep_time, dep_delay) %>%
group_by(hr) %>%
summarise(mean_delay = mean(dep_delay),count = n()) %>%
arrange(desc(mean_delay))## # A tibble: 17 × 3
## hr mean_delay count
## <dbl> <dbl> <int>
## 1 19 21.2870418 1937
## 2 17 19.9348861 3993
## 3 21 18.2857143 406
## 4 18 14.3431713 1728
## 5 15 12.3666921 2618
## 6 20 12.2851240 484
## 7 16 11.9728287 2061
## 8 14 7.7936709 1580
## 9 13 7.3642305 1683
## 10 10 5.8927536 1380
## 11 11 5.1475167 1349
## 12 12 4.9592920 2260
## 13 9 2.6576763 2410
## 14 8 2.1545312 1909
## 15 5 0.6814404 361
## 16 7 -0.4511713 3287
## 17 6 -1.0215914 2501- Pipes can be thought of as the phrase “and then”, so the above code would be read as:
- Take the input flights and then
- mutate it and then
- filter it and then
- select it and then …
- Pipes are useful when
- There is only a single input and you don’t need to combine inputs
- You only want a single ouptut and don’t care about the outputs from the intermediate steps
- But remember that without an assignment, the output is not saved to a variable
Exercises & playtime
- Using the babynames dataset from the babynames package:
- How popular was your name in the US in the year you were born, i.e. how many other babies were given the same name?
- Which are the overall most popular girl and boy baby names as measured by count? How many times more popular are they then the next most popular names?
- Since 1990 how many girls have been named “Michael”
- What was the 8th most popular year for the name “Michael” as measured by counts?
- Which girl’s name had the biggest increase in consecutive years, in what years was it, and why?
- How popular was your name in the US in the year you were born, i.e. how many other babies were given the same name?
The fivethirtyeight package has lots of fun datasets. To see the motivation behind the package’s creation as well as a description of each of the different datasets use vignette("fivethirtyeight", package = "fivethirtyeight")
Combining Data Manipulation and Visualization
- Plot the popularity of the boy’s name Brittany since 1950.
- Using the 5 most popular girl’s name from 2015 (based on counts), plot their counts over all the years recorded, using different color for each name. Now plot the same names using the prop value instead.
- Plot the number of names which have a significant share of the total names, i.e., > 1%, over all years recorded
sECTION 3 - Data Importing/Cleaning
Found vs Generated Data
- Most of the time in your research you will be using data that you or someone you know generated
- This will often result in tidy and clean data or if not at least someone you can complain to about why the data is so messy
- But what about when you have to use 3rd party data, e.g., weather information
- First you have to find the data (a topic we will not be covering)
- Then you have to import the data
- Then you have to clean and tidy the data
- Dataset formats
- Columns are variables separated by a delimeter, such as a comma (.csv), semicolon (.csv2), tab (.tsv)
- Rows are entries and their values form the index column of the data
- Usually the values in the first row are the names of the columns
# Trip Duration,Start Time,Stop Time,Start Station ID,Start Station Name
# 1893,2017-03-01 00:00:32,2017-03-01 00:32:06,2009,Catherine St & Monroe St
# 223,2017-03-01 00:01:09,2017-03-01 00:04:53,127,Barrow St & Hudson St
# 1665,2017-03-01 00:01:27,2017-03-01 00:29:12,174,E 25 St & 1 Ave
# 100,2017-03-01 00:01:29,2017-03-01 00:03:10,316,Fulton St & William St
# 1229,2017-03-01 00:01:33,2017-03-01 00:22:02,536,1 Ave & E 30 St
# 613,2017-03-01 00:01:57,2017-03-01 00:12:11,259,South St & Whitehall St
# 157,2017-03-01 00:02:12,2017-03-01 00:04:49,3329,Degraw St & Smith StCitibike Dataset
- Download the citibike_data directory from the same site where you folder where you downloaded the R file
- The RBootcamp folder in https://github.com/mseinstein/Presentations
- This dataset is publicly available online from citibike and contains every ride for an entire month
- R has a built in function for reading csv files
read.csv()which reads the data into a dataframe, but instead we will be using the tidyverse package readr, which uses the slightly differentread_csv()- Feel free to compare the documentation for the two functions if you want to know how they differ
- Since the
read_csvfunction is powerful and versatile it’s good to look at its default options before using it
# read_csv(file, col_names = TRUE, col_types = NULL,
# locale = default_locale(), na = c("", "NA"), quoted_na = TRUE,
# quote = "\"", comment = "", trim_ws = TRUE, skip = 0, n_max = Inf,
# guess_max = min(1000, n_max), progress = show_progress()) - For the file variable use the full path (‘E:\full\path\to\file.csv’)
- Note that you can easily change the working directory but that is outside the scope of this bootcamp
read_csv("./citibike_data/201701-citibike-tripdata.csv")## Parsed with column specification:
## cols(
## `Trip Duration` = col_integer(),
## `Start Time` = col_datetime(format = ""),
## `Stop Time` = col_datetime(format = ""),
## `Start Station ID` = col_integer(),
## `Start Station Name` = col_character(),
## `Start Station Latitude` = col_double(),
## `Start Station Longitude` = col_double(),
## `End Station ID` = col_integer(),
## `End Station Name` = col_character(),
## `End Station Latitude` = col_double(),
## `End Station Longitude` = col_double(),
## `Bike ID` = col_integer(),
## `User Type` = col_character(),
## `Birth Year` = col_integer(),
## Gender = col_integer()
## )## # A tibble: 726,676 × 15
## `Trip Duration` `Start Time` `Stop Time` `Start Station ID` `Start Station Name`
## <int> <dttm> <dttm> <int> <chr>
## 1 680 2017-01-01 00:00:21 2017-01-01 00:11:41 3226 W 82 St & Central Park West
## 2 1282 2017-01-01 00:00:45 2017-01-01 00:22:08 3263 Cooper Square & E 7 St
## 3 648 2017-01-01 00:00:57 2017-01-01 00:11:46 3143 5 Ave & E 78 St
## 4 631 2017-01-01 00:01:10 2017-01-01 00:11:42 3143 5 Ave & E 78 St
## 5 621 2017-01-01 00:01:25 2017-01-01 00:11:47 3143 5 Ave & E 78 St
## 6 666 2017-01-01 00:01:51 2017-01-01 00:12:57 3163 Central Park West & W 68 St
## 7 559 2017-01-01 00:05:00 2017-01-01 00:14:20 499 Broadway & W 60 St
## 8 826 2017-01-01 00:05:37 2017-01-01 00:19:24 362 Broadway & W 37 St
## 9 255 2017-01-01 00:05:47 2017-01-01 00:10:02 430 York St & Jay St
## 10 634 2017-01-01 00:07:34 2017-01-01 00:18:08 3165 Central Park West & W 72 St
## # ... with 726,666 more rows, and 10 more variables: `Start Station Latitude` <dbl>, `Start Station Longitude` <dbl>,
## # `End Station ID` <int>, `End Station Name` <chr>, `End Station Latitude` <dbl>, `End Station Longitude` <dbl>,
## # `Bike ID` <int>, `User Type` <chr>, `Birth Year` <int>, Gender <int>You can see that R solved the problem of spaces in the column names by putting ` around them (note this is a backtick not a single quote), but this makes it annoying to refer to these variables. Instead we can use a snake case version of the column names as an input into read_csv
column_names <- c("trip_duration", "start_time", "stop_time", "start_id", "start_name", "start_lat", "start_long", "end_id",
"end_name", "end_lat", "end_long", "bike_id", "user_type", "birth_year", "gender")
read_csv("./citibike_data/201701-citibike-tripdata.csv", col_names = column_names)## Parsed with column specification:
## cols(
## trip_duration = col_character(),
## start_time = col_character(),
## stop_time = col_character(),
## start_id = col_character(),
## start_name = col_character(),
## start_lat = col_character(),
## start_long = col_character(),
## end_id = col_character(),
## end_name = col_character(),
## end_lat = col_character(),
## end_long = col_character(),
## bike_id = col_character(),
## user_type = col_character(),
## birth_year = col_character(),
## gender = col_character()
## )## # A tibble: 726,677 × 15
## trip_duration start_time stop_time start_id start_name
## <chr> <chr> <chr> <chr> <chr>
## 1 Trip Duration Start Time Stop Time Start Station ID Start Station Name
## 2 680 2017-01-01 00:00:21 2017-01-01 00:11:41 3226 W 82 St & Central Park West
## 3 1282 2017-01-01 00:00:45 2017-01-01 00:22:08 3263 Cooper Square & E 7 St
## 4 648 2017-01-01 00:00:57 2017-01-01 00:11:46 3143 5 Ave & E 78 St
## 5 631 2017-01-01 00:01:10 2017-01-01 00:11:42 3143 5 Ave & E 78 St
## 6 621 2017-01-01 00:01:25 2017-01-01 00:11:47 3143 5 Ave & E 78 St
## 7 666 2017-01-01 00:01:51 2017-01-01 00:12:57 3163 Central Park West & W 68 St
## 8 559 2017-01-01 00:05:00 2017-01-01 00:14:20 499 Broadway & W 60 St
## 9 826 2017-01-01 00:05:37 2017-01-01 00:19:24 362 Broadway & W 37 St
## 10 255 2017-01-01 00:05:47 2017-01-01 00:10:02 430 York St & Jay St
## # ... with 726,667 more rows, and 10 more variables: start_lat <chr>, start_long <chr>, end_id <chr>, end_name <chr>,
## # end_lat <chr>, end_long <chr>, bike_id <chr>, user_type <chr>, birth_year <chr>, gender <chr>The problem is that when you provide the column names, read_csv treats the first row as a regular row of entries, so if we want to use our own column names we need to skip that row
citi_bike <- read_csv("./citibike_data/201701-citibike-tripdata.csv", col_names = column_names, skip = 1)## Parsed with column specification:
## cols(
## trip_duration = col_integer(),
## start_time = col_datetime(format = ""),
## stop_time = col_datetime(format = ""),
## start_id = col_integer(),
## start_name = col_character(),
## start_lat = col_double(),
## start_long = col_double(),
## end_id = col_integer(),
## end_name = col_character(),
## end_lat = col_double(),
## end_long = col_double(),
## bike_id = col_integer(),
## user_type = col_character(),
## birth_year = col_integer(),
## gender = col_integer()
## )citi_bike## # A tibble: 726,676 × 15
## trip_duration start_time stop_time start_id start_name start_lat start_long
## <int> <dttm> <dttm> <int> <chr> <dbl> <dbl>
## 1 680 2017-01-01 00:00:21 2017-01-01 00:11:41 3226 W 82 St & Central Park West 40.78275 -73.97137
## 2 1282 2017-01-01 00:00:45 2017-01-01 00:22:08 3263 Cooper Square & E 7 St 40.72924 -73.99087
## 3 648 2017-01-01 00:00:57 2017-01-01 00:11:46 3143 5 Ave & E 78 St 40.77683 -73.96389
## 4 631 2017-01-01 00:01:10 2017-01-01 00:11:42 3143 5 Ave & E 78 St 40.77683 -73.96389
## 5 621 2017-01-01 00:01:25 2017-01-01 00:11:47 3143 5 Ave & E 78 St 40.77683 -73.96389
## 6 666 2017-01-01 00:01:51 2017-01-01 00:12:57 3163 Central Park West & W 68 St 40.77341 -73.97783
## 7 559 2017-01-01 00:05:00 2017-01-01 00:14:20 499 Broadway & W 60 St 40.76916 -73.98192
## 8 826 2017-01-01 00:05:37 2017-01-01 00:19:24 362 Broadway & W 37 St 40.75173 -73.98754
## 9 255 2017-01-01 00:05:47 2017-01-01 00:10:02 430 York St & Jay St 40.70149 -73.98657
## 10 634 2017-01-01 00:07:34 2017-01-01 00:18:08 3165 Central Park West & W 72 St 40.77579 -73.97621
## # ... with 726,666 more rows, and 8 more variables: end_id <int>, end_name <chr>, end_lat <dbl>, end_long <dbl>,
## # bike_id <int>, user_type <chr>, birth_year <int>, gender <int>Parsing
- Parsing , in reference to
read_csvand similar functions, is the method of analyzing elements of a vector to determine the type of information within that vector - By default,
read_csvuses the first 1000 rows or the entire dataset, whichever is smaller, to parse each column - Usually it does a very good job and most of the time you have to change data types because you want a specific data type, not because of an error within the parser
# Let's look again at our dataset and see if all our datatypes make sense
citi_bike## # A tibble: 726,676 × 15
## trip_duration start_time stop_time start_id start_name start_lat start_long end_id end_name end_lat end_long bike_id user_type birth_year gender
## <int> <dttm> <dttm> <int> <chr> <dbl> <dbl> <int> <chr> <dbl> <dbl> <int> <chr> <int> <int>
## 1 680 2017-01-01 00:00:21 2017-01-01 00:11:41 3226 W 82 St & Central Park West 40.78275 -73.97137 3165 Central Park West & W 72 St 40.77579 -73.97621 25542 Subscriber 1965 2
## 2 1282 2017-01-01 00:00:45 2017-01-01 00:22:08 3263 Cooper Square & E 7 St 40.72924 -73.99087 498 Broadway & W 32 St 40.74855 -73.98808 21136 Subscriber 1987 2
## 3 648 2017-01-01 00:00:57 2017-01-01 00:11:46 3143 5 Ave & E 78 St 40.77683 -73.96389 3152 3 Ave & E 71 St 40.76874 -73.96120 18147 Customer NA 0
## 4 631 2017-01-01 00:01:10 2017-01-01 00:11:42 3143 5 Ave & E 78 St 40.77683 -73.96389 3152 3 Ave & E 71 St 40.76874 -73.96120 21211 Customer NA 0
## 5 621 2017-01-01 00:01:25 2017-01-01 00:11:47 3143 5 Ave & E 78 St 40.77683 -73.96389 3152 3 Ave & E 71 St 40.76874 -73.96120 26819 Customer NA 0
## 6 666 2017-01-01 00:01:51 2017-01-01 00:12:57 3163 Central Park West & W 68 St 40.77341 -73.97783 3163 Central Park West & W 68 St 40.77341 -73.97783 16050 Subscriber 2000 1
## 7 559 2017-01-01 00:05:00 2017-01-01 00:14:20 499 Broadway & W 60 St 40.76916 -73.98192 479 9 Ave & W 45 St 40.76019 -73.99126 27294 Subscriber 1973 1
## 8 826 2017-01-01 00:05:37 2017-01-01 00:19:24 362 Broadway & W 37 St 40.75173 -73.98754 445 E 10 St & Avenue A 40.72741 -73.98142 23288 Subscriber 1977 2
## 9 255 2017-01-01 00:05:47 2017-01-01 00:10:02 430 York St & Jay St 40.70149 -73.98657 242 Carlton Ave & Flushing Ave 40.69779 -73.97374 25041 Subscriber 1989 1
## 10 634 2017-01-01 00:07:34 2017-01-01 00:18:08 3165 Central Park West & W 72 St 40.77579 -73.97621 3164 Columbus Ave & W 72 St 40.77706 -73.97898 16311 Subscriber 1980 1
## # ... with 726,666 more rowssummary(citi_bike)## trip_duration start_time stop_time start_id start_name
## Min. : 61 Min. :2017-01-01 00:00:21 Min. :2017-01-01 00:10:02 Min. : 72 Length:726676
## 1st Qu.: 331 1st Qu.:2017-01-11 08:40:46 1st Qu.:2017-01-11 08:52:47 1st Qu.: 358 Class :character
## Median : 526 Median :2017-01-18 09:25:48 Median :2017-01-18 09:37:23 Median : 482 Mode :character
## Mean : 778 Mean :2017-01-17 16:36:15 Mean :2017-01-17 16:49:13 Mean :1223
## 3rd Qu.: 860 3rd Qu.:2017-01-25 15:39:17 3rd Qu.:2017-01-25 15:52:34 3rd Qu.:3092
## Max. :5325688 Max. :2017-01-31 23:59:23 Max. :2017-03-14 14:13:45 Max. :3446
##
## start_lat start_long end_id end_name end_lat end_long bike_id
## Min. : 0.00 Min. :-74.03 Min. : 72 Length:726676 Min. : 0.00 Min. :-74.03 Min. :14529
## 1st Qu.:40.72 1st Qu.:-74.00 1st Qu.: 356 Class :character 1st Qu.:40.72 1st Qu.:-74.00 1st Qu.:17859
## Median :40.74 Median :-73.99 Median : 479 Mode :character Median :40.74 Median :-73.99 Median :21295
## Mean :40.74 Mean :-73.98 Mean :1197 Mean :40.74 Mean :-73.99 Mean :21713
## 3rd Qu.:40.76 3rd Qu.:-73.98 3rd Qu.:3078 3rd Qu.:40.76 3rd Qu.:-73.98 3rd Qu.:25803
## Max. :40.80 Max. : 0.00 Max. :3447 Max. :40.80 Max. : 0.00 Max. :27325
##
## user_type birth_year gender
## Length:726676 Min. :1885 Min. :0.000
## Class :character 1st Qu.:1969 1st Qu.:1.000
## Mode :character Median :1979 Median :1.000
## Mean :1977 Mean :1.167
## 3rd Qu.:1987 3rd Qu.:1.000
## Max. :2000 Max. :2.000
## NA's :29076- Double and integers are very useful for continuous values, but when you have a limited number of discrete values (and where the orders of the valuesare typically irrelevant), the factor type is often more useful
- Factors are useful when you have a categorical variable (think of it like a dropdown menu)
- Factor values are always converted to characters
- The
level()function list all the possible options of the factor variable
- There are two ways to convert a csv tibble column into a factor
- When you initially read the file you can specify the type for each column (useful when changing most of the columns) using the
col_factor()function - After reading the file you can convert the specified columns to factors using the
as.factor()function
- When you initially read the file you can specify the type for each column (useful when changing most of the columns) using the
# In the citi_bike case start_id, end_id, user_type and gender are all variables which should be factors
citi_bike_fac <- citi_bike %>% mutate(start_id = as.factor(start_id), end_id = as.factor(end_id), user_type = as.factor(user_type),
gender = as.factor(gender))
citi_bike_fac## # A tibble: 726,676 × 15
## trip_duration start_time stop_time start_id start_name start_lat start_long
## <int> <dttm> <dttm> <fctr> <chr> <dbl> <dbl>
## 1 680 2017-01-01 00:00:21 2017-01-01 00:11:41 3226 W 82 St & Central Park West 40.78275 -73.97137
## 2 1282 2017-01-01 00:00:45 2017-01-01 00:22:08 3263 Cooper Square & E 7 St 40.72924 -73.99087
## 3 648 2017-01-01 00:00:57 2017-01-01 00:11:46 3143 5 Ave & E 78 St 40.77683 -73.96389
## 4 631 2017-01-01 00:01:10 2017-01-01 00:11:42 3143 5 Ave & E 78 St 40.77683 -73.96389
## 5 621 2017-01-01 00:01:25 2017-01-01 00:11:47 3143 5 Ave & E 78 St 40.77683 -73.96389
## 6 666 2017-01-01 00:01:51 2017-01-01 00:12:57 3163 Central Park West & W 68 St 40.77341 -73.97783
## 7 559 2017-01-01 00:05:00 2017-01-01 00:14:20 499 Broadway & W 60 St 40.76916 -73.98192
## 8 826 2017-01-01 00:05:37 2017-01-01 00:19:24 362 Broadway & W 37 St 40.75173 -73.98754
## 9 255 2017-01-01 00:05:47 2017-01-01 00:10:02 430 York St & Jay St 40.70149 -73.98657
## 10 634 2017-01-01 00:07:34 2017-01-01 00:18:08 3165 Central Park West & W 72 St 40.77579 -73.97621
## # ... with 726,666 more rows, and 8 more variables: end_id <fctr>, end_name <chr>, end_lat <dbl>, end_long <dbl>,
## # bike_id <int>, user_type <fctr>, birth_year <int>, gender <fctr>levels(citi_bike_fac$gender)## [1] "0" "1" "2"